diff --git a/codex-rs/app-server/src/effective_plugin_change.rs b/codex-rs/app-server/src/effective_plugin_change.rs
index 8c07c55dd7..1c0f394f8a 100644
--- a/codex-rs/app-server/src/effective_plugin_change.rs
+++ b/codex-rs/app-server/src/effective_plugin_change.rs
@@ -1,3 +1,4 @@
+use codex_core::McpRefreshReason;
 use std::collections::BTreeSet;
 use std::sync::Arc;
 
@@ -32,8 +33,14 @@ pub(crate) fn effective_plugins_changed_callback(
         thread_manager.skills_service().clear_cache();
 
         let refresh_thread_manager = Arc::clone(&thread_manager);
+        let reason = change.metadata_change_id.map_or(
+            McpRefreshReason::EffectivePluginsChanged,
+            McpRefreshReason::InstalledPluginMetadata,
+        );
         tokio::spawn(async move {
-            refresh_thread_manager.invalidate_mcp_runtimes().await;
+            refresh_thread_manager
+                .invalidate_mcp_runtimes_for(reason)
+                .await;
             refresh_thread_manager.refresh_hook_runtimes().await;
         });
 
diff --git a/codex-rs/app-server/src/request_processors/account_processor.rs b/codex-rs/app-server/src/request_processors/account_processor.rs
index 38bdda4260..92fb152787 100644
--- a/codex-rs/app-server/src/request_processors/account_processor.rs
+++ b/codex-rs/app-server/src/request_processors/account_processor.rs
@@ -10,6 +10,7 @@ use crate::outgoing_message::AccountNotification;
 use chrono::DateTime;
 use codex_app_server_protocol::DesktopOnboardingEntrypoint;
 use codex_app_server_protocol::GetAccountRateLimitsParams;
+use codex_core::McpRefreshReason;
 use codex_login::LoginOnboardingEntrypoint;
 use codex_login::login_with_bedrock_access_keys;
 use codex_mcp::ema_auth_scope;
@@ -297,16 +298,21 @@ impl AccountRequestProcessor {
                 Self::spawn_effective_plugins_changed_task(
                     Arc::clone(thread_manager),
                     config_manager.clone(),
+                    McpRefreshReason::AccountPluginCacheChanged,
                 );
                 let plugins_config = config.plugins_config_input();
                 let refresh_thread_manager = Arc::clone(thread_manager);
                 let refresh_config_manager = config_manager.clone();
                 let on_effective_plugins_changed: Arc<
                     dyn Fn(codex_core_plugins::EffectivePluginsChange) + Send + Sync,
-                > = Arc::new(move |_change| {
+                > = Arc::new(move |change| {
                     Self::spawn_effective_plugins_changed_task(
                         Arc::clone(&refresh_thread_manager),
                         refresh_config_manager.clone(),
+                        change.metadata_change_id.map_or(
+                            McpRefreshReason::AccountPluginCacheChanged,
+                            McpRefreshReason::InstalledPluginMetadata,
+                        ),
                     );
                 });
                 thread_manager
@@ -338,13 +344,14 @@ impl AccountRequestProcessor {
     fn spawn_effective_plugins_changed_task(
         thread_manager: Arc<ThreadManager>,
         config_manager: ConfigManager,
+        reason: McpRefreshReason,
     ) {
         tokio::spawn(async move {
             thread_manager.plugins_manager().clear_cache();
             thread_manager.skills_service().clear_cache();
             crate::mcp_refresh::reload_mcp_config_best_effort(&thread_manager, &config_manager)
                 .await;
-            thread_manager.invalidate_mcp_runtimes().await;
+            thread_manager.invalidate_mcp_runtimes_for(reason).await;
         });
     }
 
@@ -954,7 +961,9 @@ impl AccountRequestProcessor {
     }
 
     async fn send_login_success_notifications(&self, login_id: Option<Uuid>) {
-        self.thread_manager.invalidate_mcp_runtimes().await;
+        self.thread_manager
+            .invalidate_mcp_runtimes_for(McpRefreshReason::AccountLoginCompleted)
+            .await;
         self.send_account_login_notifications(AccountLoginCompletedNotification {
             login_id: login_id.map(|id| id.to_string()),
             success: true,
@@ -1016,7 +1025,9 @@ impl AccountRequestProcessor {
             self.auth_manager.reload().await;
             let auth_changes = self.auth_manager.auth_change_state_receiver();
             let owner_generation = auth_changes.borrow().owner_generation;
-            self.thread_manager.invalidate_mcp_runtimes().await;
+            self.thread_manager
+                .invalidate_mcp_runtimes_for(McpRefreshReason::AccountAuthReloaded)
+                .await;
             self.config_manager
                 .update_managed_config_loader(self.auth_manager.clone(), &self.config);
             self.config_manager
@@ -1041,7 +1052,9 @@ impl AccountRequestProcessor {
         let config =
             logout_configured_account(&self.config_manager, &self.auth_manager, &self.config)
                 .await?;
-        self.thread_manager.invalidate_mcp_runtimes().await;
+        self.thread_manager
+            .invalidate_mcp_runtimes_for(McpRefreshReason::AccountLoggedOut)
+            .await;
         clear_account_configuration(&self.config_manager, &config).await?;
 
         self.model_catalog.invalidate().await;
diff --git a/codex-rs/app-server/src/request_processors/account_processor/workspace_switching.rs b/codex-rs/app-server/src/request_processors/account_processor/workspace_switching.rs
index c518cf371b..accb051298 100644
--- a/codex-rs/app-server/src/request_processors/account_processor/workspace_switching.rs
+++ b/codex-rs/app-server/src/request_processors/account_processor/workspace_switching.rs
@@ -8,6 +8,7 @@ use codex_app_server_protocol::AccountSessionsListParams;
 use codex_app_server_protocol::AccountSessionsResponse;
 use codex_app_server_protocol::AccountSessionsSwitchParams;
 use codex_app_server_protocol::AccountSessionsSwitchResponse;
+use codex_core::McpRefreshReason;
 
 impl AccountRequestProcessor {
     pub(crate) async fn list_account_sessions(
@@ -204,7 +205,9 @@ impl AccountRequestProcessor {
                 "Workspace validation failed: {error}"
             )));
         }
-        self.thread_manager.invalidate_mcp_runtimes().await;
+        self.thread_manager
+            .invalidate_mcp_runtimes_for(McpRefreshReason::AccountWorkspaceSwitched)
+            .await;
         self.model_catalog.invalidate().await;
         Self::maybe_refresh_plugin_caches_for_current_config(
             &self.config_manager,
diff --git a/codex-rs/app-server/src/request_processors/marketplace_processor.rs b/codex-rs/app-server/src/request_processors/marketplace_processor.rs
index 5d961528cf..5932678776 100644
--- a/codex-rs/app-server/src/request_processors/marketplace_processor.rs
+++ b/codex-rs/app-server/src/request_processors/marketplace_processor.rs
@@ -1,5 +1,6 @@
 use super::*;
 use crate::plugin_config_reload;
+use codex_core::McpRefreshReason;
 
 #[derive(Clone)]
 pub(crate) struct MarketplaceRequestProcessor {
@@ -89,7 +90,9 @@ impl MarketplaceRequestProcessor {
         if !outcome.upgraded_roots.is_empty() {
             self.thread_manager.plugins_manager().clear_cache();
             self.thread_manager.skills_service().clear_cache();
-            self.thread_manager.invalidate_mcp_runtimes().await;
+            self.thread_manager
+                .invalidate_mcp_runtimes_for(McpRefreshReason::MarketplaceUpgraded)
+                .await;
             self.thread_manager.refresh_hook_runtimes().await;
         }
 
diff --git a/codex-rs/app-server/src/request_processors/mcp_processor.rs b/codex-rs/app-server/src/request_processors/mcp_processor.rs
index 2d6b065491..a7ccf1c331 100644
--- a/codex-rs/app-server/src/request_processors/mcp_processor.rs
+++ b/codex-rs/app-server/src/request_processors/mcp_processor.rs
@@ -3,6 +3,7 @@ use super::account_processor::EnterpriseLoginTarget;
 use super::thread_input::ensure_direct_input_allowed;
 use super::*;
 use codex_config::types::McpServerAuth;
+use codex_core::McpRefreshReason;
 use codex_mcp::McpServerSource;
 use codex_mcp::ReadResourceRequestParams;
 use codex_mcp::ema_auth_scope;
@@ -351,7 +352,9 @@ impl McpRequestProcessor {
                 Err(err) => (false, Some(err.to_string())),
             };
             if success && !enterprise {
-                thread_manager.invalidate_mcp_runtimes().await;
+                thread_manager
+                    .invalidate_mcp_runtimes_for(McpRefreshReason::McpOAuthLoginCompleted)
+                    .await;
             }
 
             let notification = ServerNotification::McpServerOauthLoginCompleted(
diff --git a/codex-rs/app-server/src/request_processors/plugins.rs b/codex-rs/app-server/src/request_processors/plugins.rs
index 141b8cc5fb..ed74f924a7 100644
--- a/codex-rs/app-server/src/request_processors/plugins.rs
+++ b/codex-rs/app-server/src/request_processors/plugins.rs
@@ -9,6 +9,7 @@ use codex_app_server_protocol::PluginSharePrincipalRole;
 use codex_app_server_protocol::PluginShareTargetRole;
 use codex_config::types::McpServerConfig;
 use codex_config::types::PluginsConfigToml;
+use codex_core::McpRefreshReason;
 use codex_core_plugins::OPENAI_CURATED_MARKETPLACE_NAME;
 use codex_core_plugins::PluginListBackgroundTaskOptions;
 use codex_core_plugins::PluginMarketplaceContext;
@@ -533,9 +534,11 @@ impl PluginRequestProcessor {
         Arc::clone(&self.on_effective_plugins_changed)
     }
 
-    async fn on_effective_plugins_changed(&self) {
+    async fn on_effective_plugins_changed(&self, reason: McpRefreshReason) {
         self.clear_plugin_related_caches();
-        self.thread_manager.invalidate_mcp_runtimes().await;
+        self.thread_manager
+            .invalidate_mcp_runtimes_for(reason)
+            .await;
         self.thread_manager.refresh_hook_runtimes().await;
     }
 
@@ -596,7 +599,8 @@ impl PluginRequestProcessor {
                 .refresh_non_curated_plugin_cache_for_context(&context)
                 .await
         {
-            self.on_effective_plugins_changed().await;
+            self.on_effective_plugins_changed(McpRefreshReason::NonCuratedPluginCacheRefreshed)
+                .await;
         }
         let include_vertical = context.global_config.plugins_enabled
             && marketplace_kinds.contains(&PluginListMarketplaceKind::Vertical);
@@ -875,6 +879,7 @@ impl PluginRequestProcessor {
             &context.global_config,
             auth.clone(),
             Some(self.effective_plugins_changed_callback()),
+            codex_core_plugins::InstalledPluginSyncSource::PluginInstalled,
         );
 
         let (mut data, marketplace_load_errors) = self
@@ -1584,7 +1589,9 @@ impl PluginRequestProcessor {
 
         self.clear_plugin_related_caches();
         reload_user_config(&self.config_manager, &self.thread_manager).await;
-        self.thread_manager.invalidate_mcp_runtimes().await;
+        self.thread_manager
+            .invalidate_mcp_runtimes_for(McpRefreshReason::PluginInstalled)
+            .await;
         self.thread_manager.refresh_hook_runtimes().await;
 
         let plugin_mcp_servers = load_configured_plugin_mcp_servers(
@@ -2037,7 +2044,9 @@ impl PluginRequestProcessor {
                     Err(err) => (false, Some(err.to_string())),
                 };
                 if success {
-                    thread_manager.invalidate_mcp_runtimes().await;
+                    thread_manager
+                        .invalidate_mcp_runtimes_for(McpRefreshReason::PluginOAuthLoginCompleted)
+                        .await;
                 }
 
                 let notification = ServerNotification::McpServerOauthLoginCompleted(
@@ -2074,7 +2083,10 @@ impl PluginRequestProcessor {
             .await
             .map_err(Self::plugin_uninstall_error)?;
         match self.load_latest_config(/*fallback_cwd*/ None).await {
-            Ok(_) => self.on_effective_plugins_changed().await,
+            Ok(_) => {
+                self.on_effective_plugins_changed(McpRefreshReason::PluginUninstalled)
+                    .await
+            }
             Err(err) => {
                 warn!(
                     "failed to reload config after plugin uninstall, clearing plugin-related caches only: {err:?}"
@@ -2169,7 +2181,8 @@ impl PluginRequestProcessor {
         self.analytics_events_client
             .track_plugin_uninstalled(outcome.telemetry);
         if outcome.effective_plugins_changed {
-            self.on_effective_plugins_changed().await;
+            self.on_effective_plugins_changed(McpRefreshReason::RemotePluginUninstalled)
+                .await;
         }
         if let Some(err) = outcome.cache_removal_error {
             return Err(remote_plugin_catalog_error_to_jsonrpc(
diff --git a/codex-rs/core-plugins/src/lib.rs b/codex-rs/core-plugins/src/lib.rs
index 8b8f57f836..8384333809 100644
--- a/codex-rs/core-plugins/src/lib.rs
+++ b/codex-rs/core-plugins/src/lib.rs
@@ -86,6 +86,7 @@ pub use manager::ConfiguredMarketplace;
 pub use manager::ConfiguredMarketplaceListOutcome;
 pub use manager::ConfiguredMarketplacePlugin;
 pub use manager::EffectivePluginsChange;
+pub use manager::InstalledPluginSyncSource;
 pub use manager::PluginDetail;
 pub use manager::PluginDetailsUnavailableReason;
 pub use manager::PluginInstallError;
diff --git a/codex-rs/core-plugins/src/manager.rs b/codex-rs/core-plugins/src/manager.rs
index a0845699fc..d76fe985c3 100644
--- a/codex-rs/core-plugins/src/manager.rs
+++ b/codex-rs/core-plugins/src/manager.rs
@@ -254,9 +254,19 @@ impl PluginsConfigInput {
     }
 }
 
+/// Operation that requested a background sync of installed plugin bundles.
+#[derive(Clone, Copy, Debug)]
+pub enum InstalledPluginSyncSource {
+    PluginInstalled,
+    PluginList,
+    Startup,
+}
+
 /// Effective-plugin changes that downstream composition layers may act on.
 #[derive(Debug, Clone, Default, PartialEq, Eq)]
 pub struct EffectivePluginsChange {
+    /// Joins this notification to its installed-plugin cache publication in diagnostics.
+    pub metadata_change_id: Option<uuid::Uuid>,
     /// Remote bundles installed or updated by background installed-plugin sync.
     pub materialized_remote_plugins: Vec<RemotePluginMaterialization>,
 }
@@ -320,6 +330,10 @@ struct RemoteInstalledPluginsCache {
     display_assets: InstalledPluginDisplayAssets,
 }
 
+struct InstalledPluginCacheUpdate {
+    metadata_change_id: Option<uuid::Uuid>,
+}
+
 enum RemoteInstalledPluginsCachePublication {
     Refresh(InstalledPluginDisplayAssets),
     Reconcile,
@@ -1435,7 +1449,7 @@ impl PluginsManager {
             &plugins,
             visible_marketplaces,
         );
-        let Some(changed) = self.write_remote_installed_plugins_cache_snapshot(
+        let Some(update) = self.write_remote_installed_plugins_cache_snapshot(
             generation,
             plugins,
             auth,
@@ -1453,8 +1467,13 @@ impl PluginsManager {
                 )
                 .unwrap_or(marketplaces));
         };
-        if changed && let Some(on_effective_plugins_changed) = on_effective_plugins_changed {
-            on_effective_plugins_changed(EffectivePluginsChange::default());
+        if update.metadata_change_id.is_some()
+            && let Some(on_effective_plugins_changed) = on_effective_plugins_changed
+        {
+            on_effective_plugins_changed(EffectivePluginsChange {
+                metadata_change_id: update.metadata_change_id,
+                ..Default::default()
+            });
         }
         Ok(self
             .build_remote_installed_plugin_marketplaces_from_cache_for_auth(
@@ -1545,7 +1564,7 @@ impl PluginsManager {
         plugins: Vec<RemoteInstalledPlugin>,
         auth: Option<&CodexAuth>,
         publication: RemoteInstalledPluginsCachePublication,
-    ) -> Option<bool> {
+    ) -> Option<InstalledPluginCacheUpdate> {
         let auth_identity = RemoteInstalledPluginsAuthIdentity::from_auth(auth);
         if !self.remote_installed_plugins_auth_is_current(&auth_identity) {
             return None;
@@ -1584,23 +1603,32 @@ impl PluginsManager {
                 InstalledPluginDisplayAssets::Include
             }
         };
-        if cache.plugins.as_ref() == Some(&plugins) {
-            drop(cache);
-            if needs_effective_plugins_refresh {
-                self.clear_loaded_plugins_cache();
-            }
-            return Some(needs_effective_plugins_refresh);
-        }
-        let metadata_changed = cache.plugins.as_ref().is_none_or(|previous| {
-            !crate::remote_metadata::installed_plugin_metadata_eq(previous, &plugins)
-        });
-        cache.plugins = Some(plugins);
-        drop(cache);
+        let previous = cache.plugins.as_deref();
+        let payload_changed = previous != Some(plugins.as_slice());
+        let metadata_changed = payload_changed
+            && previous.is_none_or(|old| {
+                !crate::remote_metadata::installed_plugin_metadata_eq(old, &plugins)
+            });
         let changed = needs_effective_plugins_refresh || metadata_changed;
-        if changed {
+        let metadata_change_id = changed.then(uuid::Uuid::new_v4);
+        let initial_snapshot = previous.is_none();
+        let changes = if metadata_changed && tracing::enabled!(tracing::Level::INFO) {
+            crate::remote_metadata::installed_plugin_metadata_changes(
+                previous.unwrap_or_default(),
+                &plugins,
+            )
+        } else {
+            Default::default()
+        };
+        if payload_changed {
+            cache.plugins = Some(plugins);
+        }
+        drop(cache);
+        if let Some(change_id) = metadata_change_id {
+            tracing::info!(%change_id, ?changes, initial_snapshot, reconciliation_retry = needs_effective_plugins_refresh, is_reconcile, "installed plugin runtime metadata invalidated");
             self.clear_loaded_plugins_cache();
         }
-        Some(changed)
+        Some(InstalledPluginCacheUpdate { metadata_change_id })
     }
 
     #[cfg(test)]
@@ -1616,6 +1644,8 @@ impl PluginsManager {
             RemoteInstalledPluginsCachePublication::Refresh(InstalledPluginDisplayAssets::Include),
         )
         .expect("test cache generation should remain current")
+        .metadata_change_id
+        .is_some()
     }
 
     pub fn clear_remote_installed_plugins_cache(&self) -> bool {
@@ -1727,6 +1757,7 @@ impl PluginsManager {
         config: &PluginsConfigInput,
         auth: Option<CodexAuth>,
         on_effective_plugins_changed: Option<EffectivePluginsChangedCallback>,
+        source: InstalledPluginSyncSource,
     ) {
         if !config.plugins_enabled {
             return;
@@ -1748,18 +1779,21 @@ impl PluginsManager {
                 .reconcile_remote_installed_plugins_after_acquiring_gate(&config, Some(&auth))
                 .await;
             match result {
-                Ok((outcome, effective_plugins_changed)) => {
+                Ok((outcome, update)) => {
                     tracing::info!(
                         materialized_remote_plugins = ?outcome.materialized_remote_plugins,
                         changed_plugins = ?outcome.changed_plugins,
                         failed_remote_plugin_ids = ?outcome.failed_remote_plugin_ids,
                         failed_materialization_remote_plugin_ids = ?outcome.failed_materialization_remote_plugin_ids,
+                        ?source,
+                        metadata_change_id = ?update.metadata_change_id,
                         "completed remote installed plugin bundle sync"
                     );
-                    if (effective_plugins_changed || !outcome.changed_plugins.is_empty())
+                    if (update.metadata_change_id.is_some() || !outcome.changed_plugins.is_empty())
                         && let Some(on_effective_plugins_changed) = on_effective_plugins_changed
                     {
                         on_effective_plugins_changed(EffectivePluginsChange {
+                            metadata_change_id: update.metadata_change_id,
                             materialized_remote_plugins: outcome.materialized_remote_plugins,
                         });
                     }
@@ -1817,8 +1851,13 @@ impl PluginsManager {
         &self,
         config: &PluginsConfigInput,
         auth: Option<&CodexAuth>,
-    ) -> Result<(RemoteInstalledPluginBundleSyncOutcome, bool), RemoteInstalledPluginBundleSyncError>
-    {
+    ) -> Result<
+        (
+            RemoteInstalledPluginBundleSyncOutcome,
+            InstalledPluginCacheUpdate,
+        ),
+        RemoteInstalledPluginBundleSyncError,
+    > {
         let generation = self
             .begin_remote_installed_plugins_reconcile(auth)
             .ok_or(RemoteInstalledPluginBundleSyncError::Superseded)?;
@@ -1893,7 +1932,7 @@ impl PluginsManager {
         outcome
             .changed_plugins
             .sort_unstable_by(|left, right| left.plugin_id.cmp(&right.plugin_id));
-        let Some(effective_plugins_changed) = self.write_remote_installed_plugins_cache_snapshot(
+        let Some(update) = self.write_remote_installed_plugins_cache_snapshot(
             generation,
             result.installed_plugins,
             auth,
@@ -1902,10 +1941,10 @@ impl PluginsManager {
             return Err(RemoteInstalledPluginBundleSyncError::Superseded);
         };
         reconciliation.committed = true;
-        if !effective_plugins_changed && !outcome.changed_plugins.is_empty() {
+        if update.metadata_change_id.is_none() && !outcome.changed_plugins.is_empty() {
             self.clear_loaded_plugins_cache();
         }
-        Ok((outcome, effective_plugins_changed))
+        Ok((outcome, update))
     }
 
     fn maybe_start_remote_catalog_cache_refresh(
@@ -1947,6 +1986,7 @@ impl PluginsManager {
             &context.global_config,
             auth,
             on_effective_plugins_changed,
+            InstalledPluginSyncSource::PluginList,
         );
     }
 
@@ -3041,6 +3081,7 @@ impl PluginsManager {
                     &config_for_remote_sync,
                     auth,
                     on_effective_plugins_changed,
+                    InstalledPluginSyncSource::Startup,
                 );
             });
         }
@@ -3467,7 +3508,7 @@ impl PluginsManager {
             .await;
             match plugins {
                 Ok(plugins) => {
-                    let Some(changed) = self.write_remote_installed_plugins_cache_snapshot(
+                    let Some(update) = self.write_remote_installed_plugins_cache_snapshot(
                         request.generation,
                         plugins,
                         request.auth.as_ref(),
@@ -3477,7 +3518,7 @@ impl PluginsManager {
                     ) else {
                         continue;
                     };
-                    let should_notify = changed
+                    let should_notify = update.metadata_change_id.is_some()
                         || !request.change.materialized_remote_plugins.is_empty()
                         || matches!(
                             request.notify,
@@ -3487,7 +3528,9 @@ impl PluginsManager {
                         && let Some(on_effective_plugins_changed) =
                             request.on_effective_plugins_changed
                     {
-                        on_effective_plugins_changed(request.change);
+                        let mut change = request.change;
+                        change.metadata_change_id = update.metadata_change_id;
+                        on_effective_plugins_changed(change);
                     }
                 }
                 Err(
diff --git a/codex-rs/core-plugins/src/manager_tests.rs b/codex-rs/core-plugins/src/manager_tests.rs
index c4189fdebc..c0c7ce1bd5 100644
--- a/codex-rs/core-plugins/src/manager_tests.rs
+++ b/codex-rs/core-plugins/src/manager_tests.rs
@@ -1860,12 +1860,14 @@ async fn unresolved_display_assets_does_not_satisfy_display_cache_reads() {
         .prepare_remote_installed_plugins_cache_generation(auth.as_ref())
         .unwrap();
     assert_eq!(
-        manager.write_remote_installed_plugins_cache_snapshot(
-            generation,
-            plugins.clone(),
-            auth.as_ref(),
-            RemoteInstalledPluginsCachePublication::Refresh(InstalledPluginDisplayAssets::Skip),
-        ),
+        manager
+            .write_remote_installed_plugins_cache_snapshot(
+                generation,
+                plugins.clone(),
+                auth.as_ref(),
+                RemoteInstalledPluginsCachePublication::Refresh(InstalledPluginDisplayAssets::Skip),
+            )
+            .map(|update| update.metadata_change_id.is_some()),
         Some(true)
     );
     assert!(
@@ -1883,12 +1885,16 @@ async fn unresolved_display_assets_does_not_satisfy_display_cache_reads() {
         .expect("runtime metadata is ready");
     assert_eq!(runtime[0].plugins.len(), 1);
     assert_eq!(
-        manager.write_remote_installed_plugins_cache_snapshot(
-            generation,
-            plugins.clone(),
-            auth.as_ref(),
-            RemoteInstalledPluginsCachePublication::Refresh(InstalledPluginDisplayAssets::Include),
-        ),
+        manager
+            .write_remote_installed_plugins_cache_snapshot(
+                generation,
+                plugins.clone(),
+                auth.as_ref(),
+                RemoteInstalledPluginsCachePublication::Refresh(
+                    InstalledPluginDisplayAssets::Include
+                ),
+            )
+            .map(|update| update.metadata_change_id.is_some()),
         Some(false)
     );
     assert_eq!(
@@ -1898,12 +1904,14 @@ async fn unresolved_display_assets_does_not_satisfy_display_cache_reads() {
         Some(runtime)
     );
     assert_eq!(
-        manager.write_remote_installed_plugins_cache_snapshot(
-            generation,
-            plugins,
-            auth.as_ref(),
-            RemoteInstalledPluginsCachePublication::Refresh(InstalledPluginDisplayAssets::Skip),
-        ),
+        manager
+            .write_remote_installed_plugins_cache_snapshot(
+                generation,
+                plugins,
+                auth.as_ref(),
+                RemoteInstalledPluginsCachePublication::Refresh(InstalledPluginDisplayAssets::Skip),
+            )
+            .map(|update| update.metadata_change_id.is_some()),
         Some(false)
     );
     assert!(
@@ -7454,6 +7462,7 @@ fn remote_installed_plugins_cache_refresh_coalesces_materializations() {
         authenticated_account_id: Some("account-123".to_string()),
     };
     let change = |name: &str| EffectivePluginsChange {
+        metadata_change_id: None,
         materialized_remote_plugins: vec![materialization(name)],
     };
     let callback = |count: std::sync::Arc<std::sync::atomic::AtomicUsize>| {
@@ -7496,6 +7505,7 @@ fn remote_installed_plugins_cache_refresh_coalesces_materializations() {
     assert_eq!(
         request.change,
         EffectivePluginsChange {
+            metadata_change_id: None,
             materialized_remote_plugins: vec![materialization("alpha"), materialization("beta"),],
         }
     );
@@ -7557,11 +7567,13 @@ remote_plugin = true
         &config,
         Some(auth.clone()),
         /*on_effective_plugins_changed*/ None,
+        InstalledPluginSyncSource::PluginInstalled,
     );
     second_manager.maybe_start_remote_installed_plugin_bundle_sync(
         &config,
         Some(auth),
         /*on_effective_plugins_changed*/ None,
+        InstalledPluginSyncSource::PluginInstalled,
     );
 
     let _guard = first_manager
@@ -7853,6 +7865,7 @@ async fn failed_installed_plugin_pagination_preserves_inventory_and_releases_mut
         &config,
         Some(auth),
         /*on_effective_plugins_changed*/ None,
+        InstalledPluginSyncSource::PluginInstalled,
     );
     // Starting the sync acquires the gate synchronously, so this waits for its release.
     let _guard = tokio::time::timeout(
@@ -7905,21 +7918,27 @@ fn reconciliation_fences_refresh_publication_and_recovers_after_cancellation() {
         .expect("capture concurrent refresh generation");
 
     assert_eq!(
-        manager.write_remote_installed_plugins_cache_snapshot(
-            stale_refresh_generation,
-            Vec::new(),
-            /*auth*/ None,
-            RemoteInstalledPluginsCachePublication::Refresh(InstalledPluginDisplayAssets::Include),
-        ),
+        manager
+            .write_remote_installed_plugins_cache_snapshot(
+                stale_refresh_generation,
+                Vec::new(),
+                /*auth*/ None,
+                RemoteInstalledPluginsCachePublication::Refresh(
+                    InstalledPluginDisplayAssets::Include
+                ),
+            )
+            .map(|update| update.metadata_change_id.is_some()),
         None
     );
     assert_eq!(
-        manager.write_remote_installed_plugins_cache_snapshot(
-            reconcile_generation,
-            vec![remote_installed_linear_plugin()],
-            /*auth*/ None,
-            RemoteInstalledPluginsCachePublication::Reconcile,
-        ),
+        manager
+            .write_remote_installed_plugins_cache_snapshot(
+                reconcile_generation,
+                vec![remote_installed_linear_plugin()],
+                /*auth*/ None,
+                RemoteInstalledPluginsCachePublication::Reconcile,
+            )
+            .map(|update| update.metadata_change_id.is_some()),
         Some(true)
     );
     let cancelled_generation = manager
@@ -7937,24 +7956,30 @@ fn reconciliation_fences_refresh_publication_and_recovers_after_cancellation() {
         .remote_installed_plugins_cache_generation_if_current(/*auth*/ None)
         .expect("capture refresh generation after cancellation");
     assert_eq!(
-        manager.write_remote_installed_plugins_cache_snapshot(
-            refresh_generation,
-            vec![remote_installed_plugin("beta")],
-            /*auth*/ None,
-            RemoteInstalledPluginsCachePublication::Refresh(InstalledPluginDisplayAssets::Include),
-        ),
+        manager
+            .write_remote_installed_plugins_cache_snapshot(
+                refresh_generation,
+                vec![remote_installed_plugin("beta")],
+                /*auth*/ None,
+                RemoteInstalledPluginsCachePublication::Refresh(
+                    InstalledPluginDisplayAssets::Include
+                ),
+            )
+            .map(|update| update.metadata_change_id.is_some()),
         Some(true)
     );
     let retry_generation = manager
         .begin_remote_installed_plugins_reconcile(/*auth*/ None)
         .expect("begin retry after cancellation");
     assert_eq!(
-        manager.write_remote_installed_plugins_cache_snapshot(
-            retry_generation,
-            vec![remote_installed_plugin("beta")],
-            /*auth*/ None,
-            RemoteInstalledPluginsCachePublication::Reconcile,
-        ),
+        manager
+            .write_remote_installed_plugins_cache_snapshot(
+                retry_generation,
+                vec![remote_installed_plugin("beta")],
+                /*auth*/ None,
+                RemoteInstalledPluginsCachePublication::Reconcile,
+            )
+            .map(|update| update.metadata_change_id.is_some()),
         Some(true)
     );
 }
diff --git a/codex-rs/core-plugins/src/remote_metadata.rs b/codex-rs/core-plugins/src/remote_metadata.rs
index a4db4055c1..0ab68a14c4 100644
--- a/codex-rs/core-plugins/src/remote_metadata.rs
+++ b/codex-rs/core-plugins/src/remote_metadata.rs
@@ -5,29 +5,83 @@
 
 use crate::remote::RemoteInstalledPlugin;
 use crate::remote::RemoteMarketplace;
+use std::collections::BTreeMap;
+use std::collections::HashMap;
+
+/// Use the same comparisons for invalidation and its diagnostics. Expose field names only.
+fn changed_fields<'a>(
+    previous: &'a RemoteInstalledPlugin,
+    current: &'a RemoteInstalledPlugin,
+) -> impl Iterator<Item = &'static str> + 'a {
+    macro_rules! compare {
+        ($($field:ident),+ $(,)?) => {
+            [$( (stringify!($field), previous.$field != current.$field) ),+]
+        };
+    }
+    compare!(
+        marketplace_name,
+        id,
+        name,
+        canonical_app_id,
+        version,
+        installed_at,
+        enabled,
+        install_policy,
+        install_policy_source,
+        must_show_installation_interstitial,
+        auth_policy,
+        availability,
+        disabled_reason,
+        eligible_plan_types,
+    )
+    .into_iter()
+    .filter_map(|(field, changed)| changed.then_some(field))
+}
 
 pub(crate) fn installed_plugin_metadata_eq(
     previous: &[RemoteInstalledPlugin],
     current: &[RemoteInstalledPlugin],
 ) -> bool {
     previous.len() == current.len()
-        && previous.iter().zip(current).all(|(previous, current)| {
-            previous.marketplace_name == current.marketplace_name
-                && previous.id == current.id
-                && previous.name == current.name
-                && previous.canonical_app_id == current.canonical_app_id
-                && previous.version == current.version
-                && previous.installed_at == current.installed_at
-                && previous.enabled == current.enabled
-                && previous.install_policy == current.install_policy
-                && previous.install_policy_source == current.install_policy_source
-                && previous.must_show_installation_interstitial
-                    == current.must_show_installation_interstitial
-                && previous.auth_policy == current.auth_policy
-                && previous.availability == current.availability
-                && previous.disabled_reason == current.disabled_reason
-                && previous.eligible_plan_types == current.eligible_plan_types
-        })
+        && previous
+            .iter()
+            .zip(current)
+            .all(|(previous, current)| changed_fields(previous, current).next().is_none())
+}
+
+/// Called only for a changed snapshot. Match by remote ID so an insertion does
+/// not misattribute every subsequent plugin's fields to its neighbor.
+pub(crate) fn installed_plugin_metadata_changes(
+    previous: &[RemoteInstalledPlugin],
+    current: &[RemoteInstalledPlugin],
+) -> BTreeMap<String, Vec<&'static str>> {
+    let mut old: HashMap<_, _> = previous
+        .iter()
+        .enumerate()
+        .map(|(index, p)| (p.id.as_str(), (index, p)))
+        .collect();
+    // A removed plugin shifts subsequent indices without reordering the surviving list.
+    let same_members =
+        previous.len() == current.len() && current.iter().all(|p| old.contains_key(p.id.as_str()));
+    let mut changes = BTreeMap::new();
+    for (index, plugin) in current.iter().enumerate() {
+        let fields = if let Some((old_index, prior)) = old.remove(plugin.id.as_str()) {
+            let mut fields: Vec<_> = changed_fields(prior, plugin).collect();
+            if old_index != index && same_members {
+                fields.push("position");
+            }
+            fields
+        } else {
+            vec!["added"]
+        };
+        if !fields.is_empty() {
+            changes.insert(plugin.id.clone(), fields);
+        }
+    }
+    for id in old.into_keys() {
+        changes.insert(id.to_owned(), vec!["removed"]);
+    }
+    changes
 }
 
 /// Compare installed catalog identity, versions, enablement, policy and availability.
diff --git a/codex-rs/core-plugins/src/remote_metadata_tests.rs b/codex-rs/core-plugins/src/remote_metadata_tests.rs
index 3e61f3a2ea..6397addc1d 100644
--- a/codex-rs/core-plugins/src/remote_metadata_tests.rs
+++ b/codex-rs/core-plugins/src/remote_metadata_tests.rs
@@ -121,6 +121,13 @@ fn installed_ordering_remains_significant() {
     let mut current = previous.clone();
     current.reverse();
     assert!(!installed_plugin_metadata_eq(&previous, &current));
+    assert_eq!(
+        installed_plugin_metadata_changes(&previous, &current),
+        BTreeMap::from([
+            (previous[0].id.clone(), vec!["position"]),
+            (previous[1].id.clone(), vec!["position"]),
+        ])
+    );
 }
 
 #[test]
@@ -179,3 +186,33 @@ fn catalog_display_reordering_does_not_invalidate() {
         &catalog(&current)
     ));
 }
+
+#[test]
+fn diagnostics_attribute_fields_by_plugin_id_across_membership_changes() {
+    let previous = [
+        plugin("old"),
+        RemoteInstalledPlugin {
+            id: "removed".into(),
+            ..plugin("old")
+        },
+    ];
+    let mut updated = previous[0].clone();
+    updated.enabled = !updated.enabled;
+    updated.version = Some("2".into());
+    let id = updated.id.clone();
+    let current = [
+        RemoteInstalledPlugin {
+            id: "added".into(),
+            ..plugin("new")
+        },
+        updated,
+    ];
+    assert_eq!(
+        installed_plugin_metadata_changes(&previous, &current),
+        std::collections::BTreeMap::from([
+            ("added".into(), vec!["added"]),
+            ("removed".into(), vec!["removed"]),
+            (id, vec!["version", "enabled"]),
+        ])
+    );
+}
diff --git a/codex-rs/core/src/lib.rs b/codex-rs/core/src/lib.rs
index ec127194f3..d684b39426 100644
--- a/codex-rs/core/src/lib.rs
+++ b/codex-rs/core/src/lib.rs
@@ -188,6 +188,7 @@ pub use thread_manager::AgentTreeShutdownFailureReason;
 pub use thread_manager::AgentTreeShutdownReport;
 pub use thread_manager::ForkSnapshot;
 pub use thread_manager::InternalSessionParent;
+pub use thread_manager::McpRefreshReason;
 pub use thread_manager::NewThread;
 pub use thread_manager::PromptCacheKey;
 pub use thread_manager::StartThreadOptions;
diff --git a/codex-rs/core/src/session/config_refresh.rs b/codex-rs/core/src/session/config_refresh.rs
index 016eae3978..7464df91e6 100644
--- a/codex-rs/core/src/session/config_refresh.rs
+++ b/codex-rs/core/src/session/config_refresh.rs
@@ -1,5 +1,6 @@
 //! Publishes resolved MCP configuration and host timing rollouts for future turns.
 
+use crate::McpRefreshReason;
 use std::sync::Arc;
 
 use crate::ConfigRefreshOutcome;
@@ -25,7 +26,7 @@ impl Session {
             config.disable_mcp_enterprise_auth();
             state.session_configuration.original_config_do_not_use = Arc::new(config);
             self.services.mcp_runtime.invalidate_resource_caches();
-            self.mark_mcp_runtime_dirty();
+            self.mark_mcp_runtime_dirty(McpRefreshReason::EnterpriseAuthDisabled);
         }
         self.services.mcp_runtime.quiesce_ema().await;
         self.schedule_mcp_prewarm();
@@ -192,7 +193,11 @@ impl Session {
             if matches!(scope, RuntimeConfigRefresh::Mcp) {
                 self.services.mcp_runtime.invalidate_resource_caches();
             }
-            self.mark_mcp_runtime_dirty();
+            self.mark_mcp_runtime_dirty(match scope {
+                RuntimeConfigRefresh::User => McpRefreshReason::UserConfigReloaded,
+                RuntimeConfigRefresh::Mcp => McpRefreshReason::McpConfigReloaded,
+                RuntimeConfigRefresh::UserFiles => McpRefreshReason::UserConfigFilesReloaded,
+            });
             let new_config = notify_contributors
                 .then(|| self.build_effective_session_config(&state.session_configuration));
             (previous_config, new_config)
diff --git a/codex-rs/core/src/session/environment.rs b/codex-rs/core/src/session/environment.rs
index 3820b8b7d8..e4469afbc9 100644
--- a/codex-rs/core/src/session/environment.rs
+++ b/codex-rs/core/src/session/environment.rs
@@ -1,3 +1,4 @@
+use crate::McpRefreshReason;
 use std::collections::HashSet;
 use std::sync::Arc;
 
@@ -369,7 +370,7 @@ impl Session {
         state.session_configuration.environments = future;
         if update_current {
             // Invalidate MCP before installed configuration can wake a waiting turn.
-            self.mark_mcp_runtime_dirty();
+            self.mark_mcp_runtime_dirty(McpRefreshReason::CurrentEnvironmentsChanged);
             self.services.turn_environments.update_selections(&current);
         }
         Ok(())
diff --git a/codex-rs/core/src/session/handlers.rs b/codex-rs/core/src/session/handlers.rs
index ec9ac801bf..1a4424c89e 100644
--- a/codex-rs/core/src/session/handlers.rs
+++ b/codex-rs/core/src/session/handlers.rs
@@ -1,4 +1,5 @@
 use super::Submission;
+use crate::McpRefreshReason;
 use crate::WithTurnExtensionData;
 use crate::realtime_conversation::handle_audio as handle_realtime_conversation_audio;
 use crate::realtime_conversation::handle_close as handle_realtime_conversation_close;
@@ -260,7 +261,7 @@ pub async fn dynamic_tool_response(sess: &Arc<Session>, id: String, response: Dy
 
 pub fn refresh_mcp_servers(sess: &Session) {
     sess.services.mcp_runtime.reconnect_on_next_refresh();
-    sess.request_mcp_runtime_refresh();
+    sess.request_mcp_runtime_refresh(McpRefreshReason::ExplicitServerReconnect);
 }
 
 pub async fn reload_user_config(sess: &Arc<Session>) {
diff --git a/codex-rs/core/src/session/mcp.rs b/codex-rs/core/src/session/mcp.rs
index 82aa3b8802..4865b61d38 100644
--- a/codex-rs/core/src/session/mcp.rs
+++ b/codex-rs/core/src/session/mcp.rs
@@ -1,5 +1,5 @@
-use super::mcp_refresh::McpRefreshInvalidationGuard;
 use super::*;
+use crate::McpRefreshReason;
 use crate::environment_selection::TurnEnvironmentSnapshot;
 use crate::environment_selection::combine_selected_capability_roots;
 use crate::mcp_tool_call::McpToolApprovalContext;
@@ -119,8 +119,11 @@ impl Session {
                 /*skill_turn*/ None,
             )
             .await;
-        if inventory_changed || discovery_recovered {
-            self.mark_mcp_runtime_dirty();
+        if inventory_changed {
+            self.mark_mcp_runtime_dirty(McpRefreshReason::ExecutorCapabilityInventoryChanged);
+        }
+        if discovery_recovered {
+            self.mark_mcp_runtime_dirty(McpRefreshReason::ExecutorCapabilityDiscoveryRecovered);
         }
         let mcp_projection =
             self.services
@@ -199,7 +202,7 @@ impl Session {
                 &environment_selections,
                 &environments.ready_environment_handles(),
             ) {
-                self.mark_mcp_runtime_dirty();
+                self.mark_mcp_runtime_dirty(McpRefreshReason::EnvironmentBindingsChanged);
             }
             let auth = self.services.auth_manager.auth_cached();
             if !self
@@ -207,15 +210,11 @@ impl Session {
                 .mcp_runtime
                 .current_auth_matches(auth.as_ref())
             {
-                self.mark_mcp_runtime_dirty();
+                self.mark_mcp_runtime_dirty(McpRefreshReason::RuntimeAuthChanged);
             }
 
-            if !self.mcp_refresh.claim() {
+            let Some(mut refresh_invalidation) = self.mcp_refresh.claim(self.thread_id) else {
                 return;
-            }
-            let mut refresh_invalidation = McpRefreshInvalidationGuard {
-                refresh: &self.mcp_refresh,
-                published: false,
             };
             let auth = self.services.auth_manager.auth().await;
             // Capture after claiming the refresh so a new invalidation cannot be consumed
@@ -282,7 +281,7 @@ impl Session {
         self: &Arc<Self>,
     ) -> anyhow::Result<codex_mcp::CodexAppsToolSnapshot> {
         // Reconcile unchanged config so failed or closed clients can be replaced.
-        self.mark_mcp_runtime_dirty();
+        self.mark_mcp_runtime_dirty(McpRefreshReason::CodexAppsToolRefresh);
         self.refresh_mcp_if_dirty().await;
         let _refresh = self
             .mcp_refresh
@@ -302,11 +301,9 @@ impl Session {
             .await
             .map_err(|_| anyhow::anyhow!("MCP runtime refresh semaphore closed"))?;
         // This is forced work even when there was no pending invalidation.
-        self.mcp_refresh.claim();
-        let mut refresh_invalidation = McpRefreshInvalidationGuard {
-            refresh: &self.mcp_refresh,
-            published: false,
-        };
+        let mut refresh_invalidation = self
+            .mcp_refresh
+            .claim_forced(self.thread_id, McpRefreshReason::HardRefreshCodexAppsTools);
         let auth = self.services.auth_manager.auth().await;
         let environments = self.services.turn_environments.snapshot().await;
         let environment_selections = environments.all_selections();
@@ -380,8 +377,8 @@ impl Session {
         refreshed
     }
 
-    pub(super) fn mark_mcp_runtime_dirty(&self) {
-        self.mcp_refresh.invalidate();
+    pub(super) fn mark_mcp_runtime_dirty(&self, reason: McpRefreshReason) {
+        self.mcp_refresh.invalidate(reason);
     }
 
     #[tracing::instrument(
@@ -404,7 +401,7 @@ impl Session {
             .current_ready_selected_capability_roots()
             != ready_selected_capability_roots
         {
-            self.mark_mcp_runtime_dirty();
+            self.mark_mcp_runtime_dirty(McpRefreshReason::SelectedCapabilityRootsChanged);
         }
 
         let recovered_oauth_servers =
@@ -423,7 +420,7 @@ impl Session {
                 .has_authentication_failed_servers(&recovered_oauth_servers)
                 .await
         {
-            self.mark_mcp_runtime_dirty();
+            self.mark_mcp_runtime_dirty(McpRefreshReason::OAuthCredentialsRecovered);
         }
         self.refresh_mcp_if_dirty().await;
         // Prewarm and other context-only captures must not start cloud discovery.
@@ -450,7 +447,7 @@ impl Session {
                     .await
                 {
                     // Preserve MCP updates if a later refresh is cancelled.
-                    self.mark_mcp_runtime_dirty();
+                    self.mark_mcp_runtime_dirty(McpRefreshReason::ExtensionCatalogChanged);
                 }
             }
             self.refresh_mcp_if_dirty().await;
@@ -861,11 +858,9 @@ impl Session {
             state.session_configuration.original_config_do_not_use = Arc::new(config);
         }
         // Claim after config mutation, before capturing the state this forced refresh handles.
-        self.mcp_refresh.claim();
-        let mut refresh_invalidation = McpRefreshInvalidationGuard {
-            refresh: &self.mcp_refresh,
-            published: false,
-        };
+        let mut refresh_invalidation = self
+            .mcp_refresh
+            .claim_forced(self.thread_id, McpRefreshReason::SkillMcpDependenciesAdded);
         let auth = self.services.auth_manager.auth().await;
         let ready_selected_capability_roots = self
             .services
diff --git a/codex-rs/core/src/session/mcp_prewarm.rs b/codex-rs/core/src/session/mcp_prewarm.rs
index 435699122a..49e828c863 100644
--- a/codex-rs/core/src/session/mcp_prewarm.rs
+++ b/codex-rs/core/src/session/mcp_prewarm.rs
@@ -4,17 +4,18 @@
 //! newest thread state; exact model steps remain the correctness path.
 
 use super::*;
+use crate::McpRefreshReason;
 
 impl Session {
-    pub(crate) fn request_mcp_runtime_refresh(&self) {
+    pub(crate) fn request_mcp_runtime_refresh(&self, reason: McpRefreshReason) {
         // Plugin changes can reuse connections but still change their skill resources.
         self.services.mcp_runtime.invalidate_resource_caches();
-        self.request_mcp_runtime_reprojection();
+        self.request_mcp_runtime_reprojection(reason);
     }
 
     /// Reproject contributor state without invalidating cached MCP resources.
-    pub(crate) fn request_mcp_runtime_reprojection(&self) {
-        self.mark_mcp_runtime_dirty();
+    pub(crate) fn request_mcp_runtime_reprojection(&self, reason: McpRefreshReason) {
+        self.mark_mcp_runtime_dirty(reason);
         self.schedule_mcp_prewarm();
     }
 
@@ -47,7 +48,7 @@ impl Session {
                     break;
                 };
                 if auth_changed {
-                    session.mark_mcp_runtime_dirty();
+                    session.mark_mcp_runtime_dirty(McpRefreshReason::AuthChangeNotification);
                 }
                 tokio::select! {
                     biased;
diff --git a/codex-rs/core/src/session/mcp_refresh.rs b/codex-rs/core/src/session/mcp_refresh.rs
index f70a11d157..6e33c577be 100644
--- a/codex-rs/core/src/session/mcp_refresh.rs
+++ b/codex-rs/core/src/session/mcp_refresh.rs
@@ -1,34 +1,78 @@
-use std::sync::atomic::AtomicBool;
-use std::sync::atomic::Ordering;
+use crate::McpRefreshReason;
+use codex_protocol::ThreadId;
+use std::collections::BTreeSet;
+use std::sync::Mutex;
 use tokio::sync::AcquireError;
 use tokio::sync::Semaphore;
 use tokio::sync::SemaphorePermit;
 
 /// Owns MCP invalidation and the single gate used to publish runtime updates.
 pub(super) struct McpRefresh {
-    pending: AtomicBool,
+    pending: Mutex<BTreeSet<McpRefreshReason>>,
     gate: Semaphore,
 }
 
 impl McpRefresh {
     pub(super) fn new() -> Self {
         Self {
-            pending: AtomicBool::new(false),
+            pending: Mutex::default(),
             gate: Semaphore::new(/*permits*/ 1),
         }
     }
 
-    pub(super) fn invalidate(&self) {
-        self.pending.store(true, Ordering::Release);
+    pub(super) fn invalidate(&self, reason: McpRefreshReason) {
+        self.pending
+            .lock()
+            .unwrap_or_else(std::sync::PoisonError::into_inner)
+            .insert(reason);
     }
 
     #[cfg(test)]
     pub(super) fn is_pending(&self) -> bool {
-        self.pending.load(Ordering::Acquire)
+        !self
+            .pending
+            .lock()
+            .unwrap_or_else(std::sync::PoisonError::into_inner)
+            .is_empty()
     }
 
-    pub(super) fn claim(&self) -> bool {
-        self.pending.swap(false, Ordering::AcqRel)
+    /// Take only the causes known at the start of this refresh. Later invalidations
+    /// belong to the next publication, even if they have the same cause.
+    pub(super) fn claim(&self, thread_id: ThreadId) -> Option<McpRefreshInvalidationGuard<'_>> {
+        let reasons = self.take_pending();
+        (!reasons.is_empty()).then(|| self.start(thread_id, reasons))
+    }
+
+    pub(super) fn claim_forced(
+        &self,
+        thread_id: ThreadId,
+        reason: McpRefreshReason,
+    ) -> McpRefreshInvalidationGuard<'_> {
+        let mut reasons = self.take_pending();
+        reasons.insert(reason);
+        self.start(thread_id, reasons)
+    }
+
+    pub(super) fn take_pending(&self) -> BTreeSet<McpRefreshReason> {
+        std::mem::take(
+            &mut *self
+                .pending
+                .lock()
+                .unwrap_or_else(std::sync::PoisonError::into_inner),
+        )
+    }
+
+    fn start(
+        &self,
+        thread_id: ThreadId,
+        reasons: BTreeSet<McpRefreshReason>,
+    ) -> McpRefreshInvalidationGuard<'_> {
+        tracing::info!(%thread_id, ?reasons, "refreshing MCP runtime");
+        McpRefreshInvalidationGuard {
+            refresh: self,
+            reasons,
+            published: false,
+        }
     }
 
     #[tracing::instrument(name = "mcp.runtime.refresh_wait", skip_all)]
@@ -43,14 +87,21 @@ impl McpRefresh {
 
 /// Restores a claimed refresh when its task is cancelled before publication.
 pub(super) struct McpRefreshInvalidationGuard<'a> {
-    pub(super) refresh: &'a McpRefresh,
+    refresh: &'a McpRefresh,
+    reasons: BTreeSet<McpRefreshReason>,
     pub(super) published: bool,
 }
 
 impl Drop for McpRefreshInvalidationGuard<'_> {
     fn drop(&mut self) {
         if !self.published {
-            self.refresh.invalidate();
+            let mut pending = self
+                .refresh
+                .pending
+                .lock()
+                .unwrap_or_else(std::sync::PoisonError::into_inner);
+            pending.append(&mut self.reasons);
+            pending.insert(McpRefreshReason::PreviousRefreshUnpublished);
         }
     }
 }
diff --git a/codex-rs/core/src/session/mcp_refresh_tests.rs b/codex-rs/core/src/session/mcp_refresh_tests.rs
index f6a9d5dd23..cb2d402b96 100644
--- a/codex-rs/core/src/session/mcp_refresh_tests.rs
+++ b/codex-rs/core/src/session/mcp_refresh_tests.rs
@@ -1,27 +1,36 @@
-//! Checks that successful refreshes preserve newly pending work.
+//! Verifies that refreshes consume their own causes and preserve concurrent work.
 
 use super::*;
 use pretty_assertions::assert_eq;
 
 #[test]
-fn successful_manual_claim_consumes_only_preexisting_work() {
-    for initially_pending in [false, true] {
-        for invalidated_during_refresh in [false, true] {
-            let refresh = McpRefresh::new();
-            if initially_pending {
-                refresh.invalidate();
-            }
-            assert_eq!(refresh.claim(), initially_pending);
-            let mut guard = McpRefreshInvalidationGuard {
-                refresh: &refresh,
-                published: false,
-            };
-            if invalidated_during_refresh {
-                refresh.invalidate();
-            }
-            guard.published = true;
-            drop(guard);
-            assert_eq!(refresh.is_pending(), invalidated_during_refresh);
-        }
-    }
+fn refresh_keeps_concurrent_invalidations_and_restores_unpublished_causes() {
+    let thread_id = ThreadId::new();
+    let refresh = McpRefresh::new();
+    refresh.invalidate(McpRefreshReason::McpConfigReloaded);
+    let claimed = refresh.claim(thread_id).expect("pending");
+    refresh.invalidate(McpRefreshReason::RuntimeAuthChanged);
+    drop(claimed);
+
+    let mut retry = refresh.claim(thread_id).expect("retry");
+    assert_eq!(
+        retry.reasons,
+        BTreeSet::from([
+            McpRefreshReason::RuntimeAuthChanged,
+            McpRefreshReason::McpConfigReloaded,
+            McpRefreshReason::PreviousRefreshUnpublished
+        ])
+    );
+    refresh.invalidate(McpRefreshReason::RuntimeAuthChanged);
+    retry.published = true;
+    drop(retry);
+
+    let mut next = refresh.claim(thread_id).expect("new invalidation");
+    assert_eq!(
+        next.reasons,
+        BTreeSet::from([McpRefreshReason::RuntimeAuthChanged])
+    );
+    next.published = true;
+    drop(next);
+    assert!(refresh.claim(thread_id).is_none());
 }
diff --git a/codex-rs/core/src/session/mod.rs b/codex-rs/core/src/session/mod.rs
index 9d68f4a359..3f32564982 100644
--- a/codex-rs/core/src/session/mod.rs
+++ b/codex-rs/core/src/session/mod.rs
@@ -1,5 +1,6 @@
 pub(crate) mod startup;
 
+use crate::McpRefreshReason;
 use crate::PromptCacheKey;
 use crate::WithTurnExtensionData;
 use crate::runtime_auth::RuntimeAuthSlot;
@@ -2207,7 +2208,7 @@ impl Session {
                     != updated.step_settings.service_tier;
             let mcp_inputs_changed = self.mcp_inputs_differ(&state.session_configuration, &updated);
             if mcp_inputs_changed {
-                self.mark_mcp_runtime_dirty();
+                self.mark_mcp_runtime_dirty(McpRefreshReason::SessionMcpInputsChanged);
             }
             // Save new environment defaults for future turns. The running turn keeps its own.
             windows_sandbox_changed =
@@ -4378,8 +4379,11 @@ impl Session {
                 )
                 .await
             };
-            if inventory_changed || discovery_recovered {
-                self.mark_mcp_runtime_dirty();
+            if inventory_changed {
+                self.mark_mcp_runtime_dirty(McpRefreshReason::ExecutorCapabilityInventoryChanged);
+            }
+            if discovery_recovered {
+                self.mark_mcp_runtime_dirty(McpRefreshReason::ExecutorCapabilityDiscoveryRecovered);
             }
             let extension_data =
                 codex_extension_api::ExtensionData::new(turn_context.sub_id.clone());
diff --git a/codex-rs/core/src/session/plugin_selection.rs b/codex-rs/core/src/session/plugin_selection.rs
index 0a9580db0c..99e5e3cb64 100644
--- a/codex-rs/core/src/session/plugin_selection.rs
+++ b/codex-rs/core/src/session/plugin_selection.rs
@@ -1,5 +1,6 @@
 //! Activates an admitted task's plugin selection without changing pending settings.
 
+use crate::McpRefreshReason;
 use std::sync::Arc;
 
 use super::Session;
@@ -11,7 +12,7 @@ impl Session {
             let mut state = self.state.lock().await;
             if state.active_disabled_plugin_ids != turn_context.disabled_plugin_ids {
                 state.active_disabled_plugin_ids = turn_context.disabled_plugin_ids.clone();
-                self.mark_mcp_runtime_dirty();
+                self.mark_mcp_runtime_dirty(McpRefreshReason::DisabledPluginSelectionChanged);
             }
             Arc::clone(&state.session_configuration.original_config_do_not_use)
         };
diff --git a/codex-rs/core/src/session/step_activation_tests.rs b/codex-rs/core/src/session/step_activation_tests.rs
index 4ad17f2300..1923cd29b5 100644
--- a/codex-rs/core/src/session/step_activation_tests.rs
+++ b/codex-rs/core/src/session/step_activation_tests.rs
@@ -1,4 +1,5 @@
 use super::*;
+use crate::McpRefreshReason;
 use crate::agents_md_manager::AgentsMdManager;
 use crate::agents_md_manager::SessionInstructions;
 use crate::session::Submission;
@@ -612,7 +613,7 @@ async fn submitted_sparse_updates_preserve_captured_steps_and_ordering() {
         .acquire()
         .await
         .expect("MCP refresh lock");
-    session.mark_mcp_runtime_dirty();
+    session.mark_mcp_runtime_dirty(McpRefreshReason::ExplicitInvalidation);
     let capture_cancel = CancellationToken::new();
     let mut during = Box::pin(tokio::task::unconstrained(
         session.capture_step_context(Arc::clone(&turn), &capture_cancel),
diff --git a/codex-rs/core/src/session/tests.rs b/codex-rs/core/src/session/tests.rs
index 7f96937e30..c10635e708 100644
--- a/codex-rs/core/src/session/tests.rs
+++ b/codex-rs/core/src/session/tests.rs
@@ -1,3 +1,4 @@
+use crate::McpRefreshReason;
 use crate::agent::LocalAgentControl;
 use codex_protocol::ContextWindowId;
 #[path = "compaction_replay_tests.rs"]
@@ -2329,7 +2330,7 @@ async fn refresh_config_rejects_stale_owner_without_effects(scope: RuntimeConfig
         crate::ConfigRefreshOutcome::Published
     );
     let current_owner = session.get_config().await;
-    assert!(session.mcp_refresh.claim());
+    assert!(!session.mcp_refresh.take_pending().is_empty());
 
     assert_eq!(
         session
@@ -7073,7 +7074,7 @@ pub(crate) async fn make_session_and_context() -> (Session, TurnContext) {
         "turn_id".to_string(),
         skills_snapshot,
     );
-    session.mark_mcp_runtime_dirty();
+    session.mark_mcp_runtime_dirty(McpRefreshReason::ExplicitInvalidation);
     crate::guardian::test_host::install(&session, &turn_context.config);
     (session, turn_context)
 }
@@ -9417,7 +9418,7 @@ where
         "turn_id".to_string(),
         skills_snapshot,
     ));
-    session.mark_mcp_runtime_dirty();
+    session.mark_mcp_runtime_dirty(McpRefreshReason::ExplicitInvalidation);
     crate::guardian::test_host::install(&session, &turn_context.config);
     (session, turn_context, rx_event)
 }
@@ -9604,7 +9605,7 @@ async fn refresh_mcp_servers_uses_latest_state_for_existing_turns() {
             .expect("enable secret auth storage");
         state.session_configuration.original_config_do_not_use = Arc::new(config);
     }
-    session.mark_mcp_runtime_dirty();
+    session.mark_mcp_runtime_dirty(McpRefreshReason::ExplicitInvalidation);
 
     let next_turn = session.new_default_turn().await;
     let new_step = session
@@ -9774,7 +9775,7 @@ async fn mcp_elicitation_reviewer_uses_active_reviewer_and_latest_runtime_policy
         .spawn_task(Arc::clone(&old_turn), Vec::new(), task)
         .await;
 
-    session.mark_mcp_runtime_dirty();
+    session.mark_mcp_runtime_dirty(McpRefreshReason::ExplicitInvalidation);
     session.refresh_mcp_if_dirty().await;
     if live_update {
         assert_eq!(
@@ -9990,7 +9991,7 @@ async fn mcp_elicitation_reviewer_is_reused_across_runtime_refreshes() {
     let session = Arc::new(session);
     let previous = session.mcp_elicitation_reviewer();
 
-    session.mark_mcp_runtime_dirty();
+    session.mark_mcp_runtime_dirty(McpRefreshReason::ExplicitInvalidation);
     session.refresh_mcp_if_dirty().await;
 
     assert!(Arc::ptr_eq(&previous, &session.mcp_elicitation_reviewer()));
@@ -10336,7 +10337,7 @@ async fn step_context_keeps_its_mcp_runtime_for_tools() -> anyhow::Result<()> {
     );
     assert_ne!(step_context.mcp.config().plugins, current_config.plugins);
 
-    session.mark_mcp_runtime_dirty();
+    session.mark_mcp_runtime_dirty(McpRefreshReason::ExplicitInvalidation);
     session.refresh_mcp_if_dirty().await;
     let current = session
         .services
diff --git a/codex-rs/core/src/session/turn_input_tests.rs b/codex-rs/core/src/session/turn_input_tests.rs
index 78cd5d7f01..219a4229a4 100644
--- a/codex-rs/core/src/session/turn_input_tests.rs
+++ b/codex-rs/core/src/session/turn_input_tests.rs
@@ -616,7 +616,7 @@ async fn automatic_admission_rechecks_plan_mode_without_committing_sparse_settin
         .acquire()
         .await
         .expect("acquire MCP refresh gate");
-    session.mcp_refresh.claim();
+    session.mcp_refresh.take_pending();
     assert!(!session.mcp_refresh.is_pending());
 
     for (submission_id, prepared) in [
diff --git a/codex-rs/core/src/session/turn_start_mcp_tests.rs b/codex-rs/core/src/session/turn_start_mcp_tests.rs
index 46d6ec4144..65eae0ba8c 100644
--- a/codex-rs/core/src/session/turn_start_mcp_tests.rs
+++ b/codex-rs/core/src/session/turn_start_mcp_tests.rs
@@ -1,6 +1,7 @@
 //! Turn-start MCP reconciliation, discovery cancellation, and prewarm refresh boundaries.
 
 use super::*;
+use crate::McpRefreshReason;
 use codex_mcp::McpResourceClient;
 use codex_mcp::McpResourceClientCacheKey;
 use pretty_assertions::assert_eq;
@@ -73,10 +74,10 @@ async fn turn_start_refreshes_dirty_mcp_reuses_clean_runtime_and_cancels_discove
             .requires_mcp
             .store(turn > 0, std::sync::atomic::Ordering::Relaxed);
         if turn == 0 {
-            session.mark_mcp_runtime_dirty();
+            session.mark_mcp_runtime_dirty(McpRefreshReason::ExplicitInvalidation);
         } else if turn == 3 {
             session.services.mcp_runtime.reconnect_on_next_refresh();
-            session.request_mcp_runtime_refresh();
+            session.request_mcp_runtime_refresh(McpRefreshReason::ExplicitInvalidation);
         }
         session
             .spawn_task(
diff --git a/codex-rs/core/src/tasks/mod.rs b/codex-rs/core/src/tasks/mod.rs
index af0f10df1d..5d15403492 100644
--- a/codex-rs/core/src/tasks/mod.rs
+++ b/codex-rs/core/src/tasks/mod.rs
@@ -5,6 +5,7 @@ mod regular;
 mod review;
 mod user_shell;
 
+use crate::McpRefreshReason;
 use std::sync::Arc;
 use std::time::Duration;
 use std::time::Instant;
@@ -304,7 +305,7 @@ impl Session {
             .enabled(Feature::ExecutorCapabilityDiscoveryV2)
         {
             // MCP contributors must project the new inventory even if their other inputs match.
-            self.request_mcp_runtime_reprojection();
+            self.request_mcp_runtime_reprojection(McpRefreshReason::TaskStartedExecutorDiscovery);
         }
         self.activate_plugin_selection(&turn_context).await;
         // Inherited or recovered roots are applied before task start. Otherwise this
diff --git a/codex-rs/core/src/tasks/regular.rs b/codex-rs/core/src/tasks/regular.rs
index fd91a1d557..a693630786 100644
--- a/codex-rs/core/src/tasks/regular.rs
+++ b/codex-rs/core/src/tasks/regular.rs
@@ -1,3 +1,4 @@
+use crate::McpRefreshReason;
 use std::sync::Arc;
 
 use codex_async_utils::OrCancelExt;
@@ -92,7 +93,9 @@ impl SessionTask for RegularTask {
                 .await;
             // Even cancelled discovery may have cleared the previous account's catalog.
             if prepares_mcp {
-                sess.request_mcp_runtime_reprojection();
+                sess.request_mcp_runtime_reprojection(
+                    McpRefreshReason::TurnStartContributorPreparedMcp,
+                );
             }
             if preparation.is_err() {
                 return SessionStartupPrewarmResolution::Cancelled;
diff --git a/codex-rs/core/src/thread_manager.rs b/codex-rs/core/src/thread_manager.rs
index af6c240112..18bfc6af7b 100644
--- a/codex-rs/core/src/thread_manager.rs
+++ b/codex-rs/core/src/thread_manager.rs
@@ -263,6 +263,51 @@ enum ShutdownOutcome {
     TimedOut,
 }
 
+type StartupMcpInvalidations = std::sync::Mutex<std::collections::BTreeSet<McpRefreshReason>>;
+
+/// Identifies the cause of an MCP runtime publication in CLI diagnostics.
+#[derive(Debug, Clone, Copy, PartialEq, Eq, PartialOrd, Ord)]
+pub enum McpRefreshReason {
+    AccountAuthReloaded,
+    AccountLoggedOut,
+    AccountLoginCompleted,
+    AccountPluginCacheChanged,
+    AccountWorkspaceSwitched,
+    AuthChangeNotification,
+    CodexAppsToolRefresh,
+    CurrentEnvironmentsChanged,
+    DisabledPluginSelectionChanged,
+    EffectivePluginsChanged,
+    EnterpriseAuthDisabled,
+    EnvironmentBindingsChanged,
+    ExecutorCapabilityDiscoveryRecovered,
+    ExecutorCapabilityInventoryChanged,
+    ExplicitInvalidation,
+    ExplicitServerReconnect,
+    ExtensionCatalogChanged,
+    HardRefreshCodexAppsTools,
+    MarketplaceUpgraded,
+    McpConfigReloaded,
+    McpOAuthLoginCompleted,
+    NonCuratedPluginCacheRefreshed,
+    OAuthCredentialsRecovered,
+    PluginInstalled,
+    PluginOAuthLoginCompleted,
+    PluginUninstalled,
+    PreviousRefreshUnpublished,
+    RemotePluginUninstalled,
+    RuntimeAuthChanged,
+    SelectedCapabilityRootsChanged,
+    SessionMcpInputsChanged,
+    SkillMcpDependenciesAdded,
+    TaskStartedExecutorDiscovery,
+    TurnStartContributorPreparedMcp,
+    UserConfigFilesReloaded,
+    UserConfigReloaded,
+    /// Links to the field-level diff logged when the installed plugin cache changed.
+    InstalledPluginMetadata(uuid::Uuid),
+}
+
 /// [`ThreadManager`] is responsible for creating threads and maintaining
 /// them in memory.
 pub struct ThreadManager {
@@ -545,7 +590,7 @@ pub(crate) struct ThreadManagerState {
     model_catalog: model_catalog::ThreadModelCatalog,
     git_root_discovery: Arc<GitRootDiscovery>,
     environment_manager: Arc<EnvironmentManager>,
-    starting_mcp_runtimes: std::sync::Mutex<Vec<std::sync::Weak<AtomicBool>>>,
+    starting_mcp_runtimes: std::sync::Mutex<Vec<std::sync::Weak<StartupMcpInvalidations>>>,
     skills_service: Arc<HostSkillsService>,
     plugins_manager: Arc<PluginsManager>,
     mcp_manager: Arc<McpManager>,
@@ -990,7 +1035,12 @@ impl ThreadManager {
 
     /// Refreshes every loaded thread and marks threads that are still being created.
     pub async fn invalidate_mcp_runtimes(&self) {
-        self.invalidate_starting_mcp_runtimes();
+        self.invalidate_mcp_runtimes_for(McpRefreshReason::ExplicitInvalidation)
+            .await;
+    }
+
+    pub async fn invalidate_mcp_runtimes_for(&self, reason: McpRefreshReason) {
+        self.invalidate_starting_mcp_runtimes(reason);
         let threads = self
             .state
             .threads
@@ -1000,7 +1050,7 @@ impl ThreadManager {
             .cloned()
             .collect::<Vec<_>>();
         for thread in threads {
-            thread.session.request_mcp_runtime_refresh();
+            thread.session.request_mcp_runtime_refresh(reason);
         }
     }
 
@@ -1020,7 +1070,7 @@ impl ThreadManager {
         }
     }
 
-    fn invalidate_starting_mcp_runtimes(&self) {
+    fn invalidate_starting_mcp_runtimes(&self, reason: McpRefreshReason) {
         let mut starting = self
             .state
             .starting_mcp_runtimes
@@ -1030,7 +1080,10 @@ impl ThreadManager {
             let Some(runtime) = runtime.upgrade() else {
                 return false;
             };
-            runtime.store(true, Ordering::Release);
+            runtime
+                .lock()
+                .unwrap_or_else(std::sync::PoisonError::into_inner)
+                .insert(reason);
             true
         });
     }
@@ -2702,14 +2755,14 @@ impl ThreadManagerState {
             (Arc::clone(&self.extensions), Arc::clone(&self.mcp_manager))
         };
         let tracked_session_source = session_source.clone();
-        let source_changed_during_startup = Arc::new(AtomicBool::new(false));
+        let startup_invalidations = Arc::new(StartupMcpInvalidations::default());
         {
             let mut starting = self
                 .starting_mcp_runtimes
                 .lock()
                 .unwrap_or_else(std::sync::PoisonError::into_inner);
             starting.retain(|runtime| runtime.strong_count() != 0);
-            starting.push(Arc::downgrade(&source_changed_during_startup));
+            starting.push(Arc::downgrade(&startup_invalidations));
         }
         let windows_sandbox_proxy_settings_mode = if matches!(
             &session_source,
@@ -2907,8 +2960,15 @@ impl ThreadManagerState {
         if matches!(ready_notification, ThreadReadyNotification::Emit) {
             new_thread.thread.emit_thread_ready_lifecycle().await;
         }
-        if source_changed_during_startup.load(Ordering::Acquire) {
-            new_thread.thread.session.request_mcp_runtime_refresh();
+        for reason in std::mem::take(
+            &mut *startup_invalidations
+                .lock()
+                .unwrap_or_else(std::sync::PoisonError::into_inner),
+        ) {
+            new_thread
+                .thread
+                .session
+                .request_mcp_runtime_refresh(reason);
         }
         if is_resumed_thread {
             new_thread.thread.emit_thread_resume_lifecycle().await;