diff --git a/codex-rs/app-server/src/request_processors/external_agent_session_import.rs b/codex-rs/app-server/src/request_processors/external_agent_session_import.rs
index 77b9bfcbf3..bc0a64ef72 100644
--- a/codex-rs/app-server/src/request_processors/external_agent_session_import.rs
+++ b/codex-rs/app-server/src/request_processors/external_agent_session_import.rs
@@ -215,6 +215,7 @@ impl ExternalAgentSessionImporter {
                     .unwrap_or_else(|| model_info.get_model_instructions(config.personality)),
             },
             dynamic_tools: Vec::new(),
+            selected_capability_roots: Vec::new(),
             multi_agent_version: Some(MultiAgentVersion::V1),
             initial_window_id: uuid::Uuid::now_v7().to_string(),
             metadata: ThreadPersistenceMetadata {
diff --git a/codex-rs/app-server/tests/common/rollout.rs b/codex-rs/app-server/tests/common/rollout.rs
index ec01dacc47..8d2567c010 100644
--- a/codex-rs/app-server/tests/common/rollout.rs
+++ b/codex-rs/app-server/tests/common/rollout.rs
@@ -200,6 +200,7 @@ fn create_fake_rollout_with_source_and_parent_thread_id(
         model_provider: model_provider.map(str::to_string),
         base_instructions: None,
         dynamic_tools: None,
+        selected_capability_roots: Vec::new(),
         memory_mode: None,
         multi_agent_version: None,
         context_window: None,
@@ -288,6 +289,7 @@ pub fn create_fake_rollout_with_text_elements(
         model_provider: model_provider.map(str::to_string),
         base_instructions: None,
         dynamic_tools: None,
+        selected_capability_roots: Vec::new(),
         memory_mode: None,
         multi_agent_version: None,
         context_window: None,
diff --git a/codex-rs/app-server/tests/suite/conversation_summary.rs b/codex-rs/app-server/tests/suite/conversation_summary.rs
index 7f964d3147..63ad473261 100644
--- a/codex-rs/app-server/tests/suite/conversation_summary.rs
+++ b/codex-rs/app-server/tests/suite/conversation_summary.rs
@@ -131,6 +131,7 @@ async fn get_conversation_summary_by_thread_id_reads_pathless_store_thread() ->
             originator: "test_originator".to_string(),
             base_instructions: BaseInstructions::default(),
             dynamic_tools: Vec::new(),
+            selected_capability_roots: Vec::new(),
             multi_agent_version: None,
             initial_window_id: Uuid::now_v7().to_string(),
             metadata: ThreadPersistenceMetadata {
diff --git a/codex-rs/app-server/tests/suite/v2/remote_thread_store.rs b/codex-rs/app-server/tests/suite/v2/remote_thread_store.rs
index 8fdb38e5ea..7e0db1b5b3 100644
--- a/codex-rs/app-server/tests/suite/v2/remote_thread_store.rs
+++ b/codex-rs/app-server/tests/suite/v2/remote_thread_store.rs
@@ -158,6 +158,7 @@ async fn thread_delete_with_non_local_thread_store_does_not_create_local_persist
             originator: "test_originator".to_string(),
             base_instructions: BaseInstructions::default(),
             dynamic_tools: Vec::new(),
+            selected_capability_roots: Vec::new(),
             multi_agent_version: None,
             initial_window_id: Uuid::now_v7().to_string(),
             metadata: ThreadPersistenceMetadata {
diff --git a/codex-rs/app-server/tests/suite/v2/thread_read.rs b/codex-rs/app-server/tests/suite/v2/thread_read.rs
index 6b427b0d97..9f67761757 100644
--- a/codex-rs/app-server/tests/suite/v2/thread_read.rs
+++ b/codex-rs/app-server/tests/suite/v2/thread_read.rs
@@ -1369,6 +1369,7 @@ async fn seed_pathless_store_thread(
             originator: "test_originator".to_string(),
             base_instructions: BaseInstructions::default(),
             dynamic_tools: Vec::new(),
+            selected_capability_roots: Vec::new(),
             multi_agent_version: None,
             initial_window_id: Uuid::now_v7().to_string(),
             metadata: ThreadPersistenceMetadata {
diff --git a/codex-rs/app-server/tests/suite/v2/thread_resume.rs b/codex-rs/app-server/tests/suite/v2/thread_resume.rs
index ce95f4810c..533087a11e 100644
--- a/codex-rs/app-server/tests/suite/v2/thread_resume.rs
+++ b/codex-rs/app-server/tests/suite/v2/thread_resume.rs
@@ -2070,6 +2070,7 @@ stream_max_retries = 0
         model_provider: Some("mock_provider".to_string()),
         base_instructions: None,
         dynamic_tools: None,
+        selected_capability_roots: Vec::new(),
         memory_mode: None,
         multi_agent_version: None,
         context_window: None,
diff --git a/codex-rs/app-server/tests/suite/v2/thread_unarchive.rs b/codex-rs/app-server/tests/suite/v2/thread_unarchive.rs
index f647dc2cfd..231ede47b9 100644
--- a/codex-rs/app-server/tests/suite/v2/thread_unarchive.rs
+++ b/codex-rs/app-server/tests/suite/v2/thread_unarchive.rs
@@ -218,6 +218,7 @@ async fn thread_unarchive_preserves_pathless_store_metadata() -> Result<()> {
             originator: "test_originator".to_string(),
             base_instructions: BaseInstructions::default(),
             dynamic_tools: Vec::new(),
+            selected_capability_roots: Vec::new(),
             multi_agent_version: None,
             initial_window_id: Uuid::now_v7().to_string(),
             metadata: ThreadPersistenceMetadata {
diff --git a/codex-rs/core/src/personality_migration_tests.rs b/codex-rs/core/src/personality_migration_tests.rs
index dd0da327c4..396d065644 100644
--- a/codex-rs/core/src/personality_migration_tests.rs
+++ b/codex-rs/core/src/personality_migration_tests.rs
@@ -59,6 +59,7 @@ async fn write_rollout_with_user_event(dir: &Path, thread_id: ThreadId) -> io::R
             model_provider: None,
             base_instructions: None,
             dynamic_tools: None,
+            selected_capability_roots: Vec::new(),
             memory_mode: None,
             multi_agent_version: None,
             context_window: None,
diff --git a/codex-rs/core/src/session/session.rs b/codex-rs/core/src/session/session.rs
index e43a26bbe5..54b531328a 100644
--- a/codex-rs/core/src/session/session.rs
+++ b/codex-rs/core/src/session/session.rs
@@ -10,6 +10,7 @@ use crate::state::ActiveTurn;
 use codex_extension_api::ExtensionDataInit;
 use codex_login::auth::AgentIdentityAuthPolicy;
 use codex_protocol::SessionId;
+use codex_protocol::capabilities::SelectedCapabilityRoot;
 use codex_protocol::config_types::SERVICE_TIER_DEFAULT_REQUEST_VALUE;
 use codex_protocol::config_types::ServiceTier;
 use codex_protocol::permissions::FileSystemPath;
@@ -555,6 +556,10 @@ impl Session {
             config.current_time_reminder.as_ref(),
             external_time_provider,
         )?;
+        let selected_capability_roots = thread_extension_init
+            .get::<Vec<SelectedCapabilityRoot>>()
+            .map(|roots| roots.as_ref().clone())
+            .unwrap_or_else(|| initial_history.get_selected_capability_roots());
         let mcp_thread_init = thread_extension_init.clone();
         let thread_extension_data = codex_extension_api::ExtensionData::new_with_init(
             thread_id.to_string(),
@@ -584,6 +589,7 @@ impl Session {
                                 text: session_configuration.base_instructions.clone(),
                             },
                             dynamic_tools: session_configuration.dynamic_tools.clone(),
+                            selected_capability_roots: selected_capability_roots.clone(),
                             multi_agent_version: initial_multi_agent_version,
                             initial_window_id: initial_auto_compact_window_ids
                                 .window_id
diff --git a/codex-rs/core/src/session/tests.rs b/codex-rs/core/src/session/tests.rs
index 4553d54a0c..c83b26d098 100644
--- a/codex-rs/core/src/session/tests.rs
+++ b/codex-rs/core/src/session/tests.rs
@@ -4043,6 +4043,7 @@ async fn attach_thread_persistence(session: &mut Session) -> PathBuf {
             originator: "test_originator".to_string(),
             base_instructions: BaseInstructions::default(),
             dynamic_tools: Vec::new(),
+            selected_capability_roots: Vec::new(),
             multi_agent_version: None,
             initial_window_id: Uuid::now_v7().to_string(),
             metadata: ThreadPersistenceMetadata {
@@ -6919,6 +6920,7 @@ async fn shutdown_complete_does_not_append_to_thread_store_after_shutdown() {
             originator: "test_originator".to_string(),
             base_instructions: BaseInstructions::default(),
             dynamic_tools: Vec::new(),
+            selected_capability_roots: Vec::new(),
             multi_agent_version: None,
             initial_window_id: Uuid::now_v7().to_string(),
             metadata: ThreadPersistenceMetadata {
diff --git a/codex-rs/core/src/thread_manager_tests.rs b/codex-rs/core/src/thread_manager_tests.rs
index f1acc2d979..b230eb12bb 100644
--- a/codex-rs/core/src/thread_manager_tests.rs
+++ b/codex-rs/core/src/thread_manager_tests.rs
@@ -20,6 +20,8 @@ use codex_protocol::protocol::AgentMessageEvent;
 use codex_protocol::protocol::InitialHistory;
 use codex_protocol::protocol::InternalSessionSource;
 use codex_protocol::protocol::ResumedHistory;
+use codex_protocol::protocol::SessionMeta;
+use codex_protocol::protocol::SessionMetaLine;
 use codex_protocol::protocol::SessionSource;
 use codex_protocol::protocol::ThreadSource;
 use codex_protocol::protocol::TurnStartedEvent;
@@ -610,6 +612,110 @@ async fn start_thread_seeds_extension_data_for_mcp_and_lifecycle_contributors()
     );
 }
 
+#[tokio::test]
+async fn selected_capability_roots_round_trip_through_fork_and_explicit_empty_wins() {
+    let temp_dir = tempdir().expect("tempdir");
+    let mut config = test_config().await;
+    config.codex_home = temp_dir.path().join("codex-home").abs();
+    config.cwd = config.codex_home.abs();
+    std::fs::create_dir_all(&config.codex_home).expect("create codex home");
+
+    let manager = ThreadManager::with_models_provider_and_home_for_tests(
+        CodexAuth::from_api_key("dummy"),
+        config.model_provider.clone(),
+        config.codex_home.to_path_buf(),
+        Arc::new(codex_exec_server::EnvironmentManager::default_for_tests()),
+    );
+    let selected_roots = vec![SelectedCapabilityRoot {
+        id: "demo@1".to_string(),
+        location: CapabilityRootLocation::Environment {
+            environment_id: "build".to_string(),
+            path: PathUri::parse("file:///plugins/demo").expect("plugin root URI"),
+        },
+    }];
+    let fork_history = || {
+        InitialHistory::Forked(vec![RolloutItem::SessionMeta(SessionMetaLine {
+            meta: SessionMeta {
+                selected_capability_roots: selected_roots.clone(),
+                ..SessionMeta::default()
+            },
+            git: None,
+        })])
+    };
+
+    let inherited = manager
+        .start_thread_with_options(StartThreadOptions {
+            config: config.clone(),
+            initial_history: fork_history(),
+            session_source: None,
+            thread_source: None,
+            dynamic_tools: Vec::new(),
+            metrics_service_name: None,
+            parent_trace: None,
+            environments: Vec::new(),
+            thread_extension_init: Default::default(),
+            supports_openai_form_elicitation: false,
+        })
+        .await
+        .expect("start inherited fork");
+    inherited.thread.ensure_rollout_materialized().await;
+    inherited
+        .thread
+        .flush_rollout()
+        .await
+        .expect("flush inherited fork");
+    let inherited_history = RolloutRecorder::get_rollout_history(
+        &inherited
+            .thread
+            .rollout_path()
+            .expect("inherited fork rollout path"),
+    )
+    .await
+    .expect("read inherited fork rollout");
+
+    assert_eq!(
+        inherited_history.get_selected_capability_roots(),
+        selected_roots
+    );
+
+    let mut explicit_empty = codex_extension_api::ExtensionDataInit::new();
+    explicit_empty.insert(Vec::<SelectedCapabilityRoot>::new());
+    let overridden = manager
+        .start_thread_with_options(StartThreadOptions {
+            config,
+            initial_history: fork_history(),
+            session_source: None,
+            thread_source: None,
+            dynamic_tools: Vec::new(),
+            metrics_service_name: None,
+            parent_trace: None,
+            environments: Vec::new(),
+            thread_extension_init: explicit_empty,
+            supports_openai_form_elicitation: false,
+        })
+        .await
+        .expect("start explicitly empty fork");
+    overridden.thread.ensure_rollout_materialized().await;
+    overridden
+        .thread
+        .flush_rollout()
+        .await
+        .expect("flush explicitly empty fork");
+    let overridden_history = RolloutRecorder::get_rollout_history(
+        &overridden
+            .thread
+            .rollout_path()
+            .expect("explicitly empty fork rollout path"),
+    )
+    .await
+    .expect("read explicitly empty fork rollout");
+
+    assert_eq!(
+        overridden_history.get_selected_capability_roots(),
+        Vec::new()
+    );
+}
+
 #[tokio::test]
 async fn resume_and_fork_do_not_restore_thread_environments_from_rollout() {
     let temp_dir = tempdir().expect("tempdir");
diff --git a/codex-rs/core/tests/suite/personality_migration.rs b/codex-rs/core/tests/suite/personality_migration.rs
index ca1d148728..3dd0f3c016 100644
--- a/codex-rs/core/tests/suite/personality_migration.rs
+++ b/codex-rs/core/tests/suite/personality_migration.rs
@@ -75,6 +75,7 @@ async fn write_rollout_with_user_event(dir: &Path, thread_id: ThreadId) -> io::R
             model_provider: None,
             base_instructions: None,
             dynamic_tools: None,
+            selected_capability_roots: Vec::new(),
             memory_mode: None,
             multi_agent_version: None,
             context_window: None,
@@ -127,6 +128,7 @@ async fn write_rollout_with_meta_only(dir: &Path, thread_id: ThreadId) -> io::Re
             model_provider: None,
             base_instructions: None,
             dynamic_tools: None,
+            selected_capability_roots: Vec::new(),
             memory_mode: None,
             multi_agent_version: None,
             context_window: None,
diff --git a/codex-rs/core/tests/suite/sqlite_state.rs b/codex-rs/core/tests/suite/sqlite_state.rs
index 5eea5a09e7..1c2f08262a 100644
--- a/codex-rs/core/tests/suite/sqlite_state.rs
+++ b/codex-rs/core/tests/suite/sqlite_state.rs
@@ -372,6 +372,7 @@ async fn backfill_scans_existing_rollouts() -> Result<()> {
                     model_provider: None,
                     base_instructions: None,
                     dynamic_tools: None,
+                    selected_capability_roots: Vec::new(),
                     memory_mode: None,
                     multi_agent_version: None,
                     context_window: None,
diff --git a/codex-rs/protocol/src/protocol.rs b/codex-rs/protocol/src/protocol.rs
index 1affdf0d20..42b01b16f3 100644
--- a/codex-rs/protocol/src/protocol.rs
+++ b/codex-rs/protocol/src/protocol.rs
@@ -19,6 +19,7 @@ use crate::AgentPath;
 use crate::SessionId;
 use crate::ThreadId;
 use crate::approvals::ElicitationRequestEvent;
+use crate::capabilities::SelectedCapabilityRoot;
 use crate::config_types::ApprovalsReviewer;
 use crate::config_types::CollaborationMode;
 use crate::config_types::ModeKind;
@@ -2570,6 +2571,12 @@ impl InitialHistory {
         }
     }
 
+    pub fn get_selected_capability_roots(&self) -> Vec<SelectedCapabilityRoot> {
+        self.get_session_meta()
+            .map(|meta| meta.selected_capability_roots.clone())
+            .unwrap_or_default()
+    }
+
     pub fn get_multi_agent_version(&self) -> Option<MultiAgentVersion> {
         match self {
             InitialHistory::New | InitialHistory::Cleared => None,
@@ -3003,6 +3010,9 @@ pub struct SessionMeta {
         skip_serializing_if = "Option::is_none"
     )]
     pub dynamic_tools: Option<Vec<DynamicToolSpec>>,
+    /// Capability roots selected for this thread by the hosting platform.
+    #[serde(default, skip_serializing_if = "Vec::is_empty")]
+    pub selected_capability_roots: Vec<SelectedCapabilityRoot>,
     #[serde(skip_serializing_if = "Option::is_none")]
     pub memory_mode: Option<String>,
     #[serde(skip_serializing_if = "Option::is_none")]
@@ -3032,6 +3042,7 @@ impl Default for SessionMeta {
             model_provider: None,
             base_instructions: None,
             dynamic_tools: None,
+            selected_capability_roots: Vec::new(),
             memory_mode: None,
             multi_agent_version: None,
             context_window: None,
diff --git a/codex-rs/rollout/src/compression_tests.rs b/codex-rs/rollout/src/compression_tests.rs
index a4db9a965c..733e6cc5fb 100644
--- a/codex-rs/rollout/src/compression_tests.rs
+++ b/codex-rs/rollout/src/compression_tests.rs
@@ -472,6 +472,7 @@ fn write_rollout(path: &std::path::Path, thread_id: ThreadId, message: &str) ->
             model_provider: None,
             base_instructions: None,
             dynamic_tools: None,
+            selected_capability_roots: Vec::new(),
             memory_mode: None,
             multi_agent_version: None,
             context_window: None,
diff --git a/codex-rs/rollout/src/metadata_tests.rs b/codex-rs/rollout/src/metadata_tests.rs
index 0744e7780e..c0aea248c5 100644
--- a/codex-rs/rollout/src/metadata_tests.rs
+++ b/codex-rs/rollout/src/metadata_tests.rs
@@ -49,6 +49,7 @@ async fn extract_metadata_from_rollout_uses_session_meta() {
         model_provider: Some("openai".to_string()),
         base_instructions: None,
         dynamic_tools: None,
+        selected_capability_roots: Vec::new(),
         memory_mode: None,
         multi_agent_version: None,
         context_window: None,
@@ -106,6 +107,7 @@ async fn extract_metadata_from_rollout_returns_latest_memory_mode() {
         model_provider: Some("openai".to_string()),
         base_instructions: None,
         dynamic_tools: None,
+        selected_capability_roots: Vec::new(),
         memory_mode: None,
         multi_agent_version: None,
         context_window: None,
@@ -375,6 +377,7 @@ fn write_rollout_in_sessions_with_cwd(
         model_provider: Some("test-provider".to_string()),
         base_instructions: None,
         dynamic_tools: None,
+        selected_capability_roots: Vec::new(),
         memory_mode: None,
         multi_agent_version: None,
         context_window: None,
diff --git a/codex-rs/rollout/src/recorder.rs b/codex-rs/rollout/src/recorder.rs
index 3908604c77..58d5c76662 100644
--- a/codex-rs/rollout/src/recorder.rs
+++ b/codex-rs/rollout/src/recorder.rs
@@ -12,6 +12,7 @@ use std::sync::Mutex;
 use chrono::SecondsFormat;
 use codex_protocol::SessionId;
 use codex_protocol::ThreadId;
+use codex_protocol::capabilities::SelectedCapabilityRoot;
 use codex_protocol::dynamic_tools::DynamicToolSpec;
 use codex_protocol::models::BaseInstructions;
 use serde_json::Value;
@@ -91,6 +92,7 @@ pub enum RolloutRecorderParams {
         originator: String,
         base_instructions: BaseInstructions,
         dynamic_tools: Vec<DynamicToolSpec>,
+        selected_capability_roots: Vec<SelectedCapabilityRoot>,
         multi_agent_version: Option<MultiAgentVersion>,
         initial_window_id: Option<String>,
     },
@@ -182,6 +184,7 @@ impl RolloutRecorderParams {
             originator,
             base_instructions,
             dynamic_tools,
+            selected_capability_roots: Vec::new(),
             multi_agent_version: None,
             initial_window_id: None,
         }
@@ -194,6 +197,20 @@ impl RolloutRecorderParams {
         self
     }
 
+    pub fn with_selected_capability_roots(
+        mut self,
+        selected_capability_roots: Vec<SelectedCapabilityRoot>,
+    ) -> Self {
+        if let Self::Create {
+            selected_capability_roots: roots,
+            ..
+        } = &mut self
+        {
+            *roots = selected_capability_roots;
+        }
+        self
+    }
+
     pub fn with_multi_agent_version(
         mut self,
         multi_agent_version: Option<MultiAgentVersion>,
@@ -732,6 +749,7 @@ impl RolloutRecorder {
                 originator,
                 base_instructions,
                 dynamic_tools,
+                selected_capability_roots,
                 multi_agent_version,
                 initial_window_id,
             } => {
@@ -769,6 +787,7 @@ impl RolloutRecorder {
                     } else {
                         Some(dynamic_tools)
                     },
+                    selected_capability_roots,
                     memory_mode: (!config.generate_memories()).then_some("disabled".to_string()),
                     multi_agent_version,
                     context_window: initial_window_id.map(SessionContextWindow::new),
diff --git a/codex-rs/rollout/src/recorder_tests.rs b/codex-rs/rollout/src/recorder_tests.rs
index 4b72ff7673..71ec252c23 100644
--- a/codex-rs/rollout/src/recorder_tests.rs
+++ b/codex-rs/rollout/src/recorder_tests.rs
@@ -101,6 +101,7 @@ async fn state_db_init_backfills_before_returning() -> anyhow::Result<()> {
             model_provider: None,
             base_instructions: None,
             dynamic_tools: None,
+            selected_capability_roots: Vec::new(),
             memory_mode: None,
             multi_agent_version: None,
             context_window: None,
diff --git a/codex-rs/rollout/src/session_index_tests.rs b/codex-rs/rollout/src/session_index_tests.rs
index 7f57c2ba08..be39fb06ab 100644
--- a/codex-rs/rollout/src/session_index_tests.rs
+++ b/codex-rs/rollout/src/session_index_tests.rs
@@ -41,6 +41,7 @@ fn write_rollout_with_metadata(path: &Path, thread_id: ThreadId) -> std::io::Res
                 model_provider: Some("test-provider".into()),
                 base_instructions: None,
                 dynamic_tools: None,
+                selected_capability_roots: Vec::new(),
                 memory_mode: None,
                 multi_agent_version: None,
                 context_window: None,
diff --git a/codex-rs/rollout/src/state_db_tests.rs b/codex-rs/rollout/src/state_db_tests.rs
index 5712b65cee..bb341aa85a 100644
--- a/codex-rs/rollout/src/state_db_tests.rs
+++ b/codex-rs/rollout/src/state_db_tests.rs
@@ -174,6 +174,7 @@ fn write_rollout_with_user_message(
                     model_provider: Some("test-provider".to_string()),
                     base_instructions: None,
                     dynamic_tools: None,
+                    selected_capability_roots: Vec::new(),
                     memory_mode: None,
                     multi_agent_version: None,
                     context_window: None,
diff --git a/codex-rs/rollout/src/tests.rs b/codex-rs/rollout/src/tests.rs
index e6a3c728ef..901461cf56 100644
--- a/codex-rs/rollout/src/tests.rs
+++ b/codex-rs/rollout/src/tests.rs
@@ -1288,6 +1288,7 @@ async fn test_updated_at_uses_file_mtime() -> Result<()> {
                 model_provider: Some("test-provider".into()),
                 base_instructions: None,
                 dynamic_tools: None,
+                selected_capability_roots: Vec::new(),
                 memory_mode: None,
                 multi_agent_version: None,
                 context_window: None,
diff --git a/codex-rs/state/src/extract.rs b/codex-rs/state/src/extract.rs
index e5ae07839e..81de0cc39f 100644
--- a/codex-rs/state/src/extract.rs
+++ b/codex-rs/state/src/extract.rs
@@ -343,6 +343,7 @@ mod tests {
                     model_provider: Some("openai".to_string()),
                     base_instructions: None,
                     dynamic_tools: None,
+                    selected_capability_roots: Vec::new(),
                     memory_mode: None,
                     multi_agent_version: None,
                     context_window: None,
@@ -535,6 +536,7 @@ mod tests {
                     model_provider: Some("openai".to_string()),
                     base_instructions: None,
                     dynamic_tools: None,
+                    selected_capability_roots: Vec::new(),
                     memory_mode: None,
                     multi_agent_version: None,
                     context_window: None,
diff --git a/codex-rs/state/src/runtime/threads.rs b/codex-rs/state/src/runtime/threads.rs
index d1c2c90762..e5ab6fb31d 100644
--- a/codex-rs/state/src/runtime/threads.rs
+++ b/codex-rs/state/src/runtime/threads.rs
@@ -2148,6 +2148,7 @@ mod tests {
                 model_provider: None,
                 base_instructions: None,
                 dynamic_tools: None,
+                selected_capability_roots: Vec::new(),
                 memory_mode: Some("polluted".to_string()),
                 multi_agent_version: None,
                 context_window: None,
@@ -2211,6 +2212,7 @@ mod tests {
                 model_provider: None,
                 base_instructions: None,
                 dynamic_tools: None,
+                selected_capability_roots: Vec::new(),
                 memory_mode: None,
                 multi_agent_version: None,
                 context_window: None,
diff --git a/codex-rs/thread-store/src/in_memory.rs b/codex-rs/thread-store/src/in_memory.rs
index dfed2ffac2..d64510f223 100644
--- a/codex-rs/thread-store/src/in_memory.rs
+++ b/codex-rs/thread-store/src/in_memory.rs
@@ -126,6 +126,7 @@ mod tests {
                     originator: "test_originator".to_string(),
                     base_instructions: BaseInstructions::default(),
                     dynamic_tools: Vec::new(),
+                    selected_capability_roots: Vec::new(),
                     multi_agent_version: None,
                     initial_window_id: uuid::Uuid::now_v7().to_string(),
                     metadata: ThreadPersistenceMetadata {
@@ -281,6 +282,7 @@ impl InMemoryThreadStore {
             model_provider: Some(params.metadata.model_provider.clone()),
             base_instructions: Some(params.base_instructions.clone()),
             dynamic_tools: (!params.dynamic_tools.is_empty()).then(|| params.dynamic_tools.clone()),
+            selected_capability_roots: params.selected_capability_roots.clone(),
             memory_mode: matches!(params.metadata.memory_mode, ThreadMemoryMode::Disabled)
                 .then_some("disabled".to_string()),
             multi_agent_version: params.multi_agent_version,
diff --git a/codex-rs/thread-store/src/local/create_thread.rs b/codex-rs/thread-store/src/local/create_thread.rs
index eba6a5a6a9..451931b4dc 100644
--- a/codex-rs/thread-store/src/local/create_thread.rs
+++ b/codex-rs/thread-store/src/local/create_thread.rs
@@ -38,6 +38,7 @@ pub(super) async fn create_thread(
             params.dynamic_tools,
         )
         .with_session_id(params.session_id)
+        .with_selected_capability_roots(params.selected_capability_roots)
         .with_multi_agent_version(params.multi_agent_version)
         .with_initial_window_id(params.initial_window_id),
     )
diff --git a/codex-rs/thread-store/src/local/mod.rs b/codex-rs/thread-store/src/local/mod.rs
index 51e622fc5b..717ae09b69 100644
--- a/codex-rs/thread-store/src/local/mod.rs
+++ b/codex-rs/thread-store/src/local/mod.rs
@@ -1133,6 +1133,7 @@ mod tests {
             originator: "test_originator".to_string(),
             base_instructions: BaseInstructions::default(),
             dynamic_tools: Vec::new(),
+            selected_capability_roots: Vec::new(),
             multi_agent_version: None,
             initial_window_id: uuid::Uuid::now_v7().to_string(),
             metadata: thread_metadata(),
diff --git a/codex-rs/thread-store/src/types.rs b/codex-rs/thread-store/src/types.rs
index 1f761cea93..f96a4df31b 100644
--- a/codex-rs/thread-store/src/types.rs
+++ b/codex-rs/thread-store/src/types.rs
@@ -5,6 +5,7 @@ use chrono::DateTime;
 use chrono::Utc;
 use codex_protocol::SessionId;
 use codex_protocol::ThreadId;
+use codex_protocol::capabilities::SelectedCapabilityRoot;
 use codex_protocol::dynamic_tools::DynamicToolSpec;
 use codex_protocol::models::BaseInstructions;
 use codex_protocol::models::PermissionProfile;
@@ -85,6 +86,9 @@ pub struct CreateThreadParams {
     pub base_instructions: BaseInstructions,
     /// Dynamic tools available to the thread at startup.
     pub dynamic_tools: Vec<DynamicToolSpec>,
+    /// Environment-qualified capability roots selected for this thread.
+    #[serde(default, skip_serializing_if = "Vec::is_empty")]
+    pub selected_capability_roots: Vec<SelectedCapabilityRoot>,
     /// Multi-agent runtime selected when the thread was created.
     pub multi_agent_version: Option<MultiAgentVersion>,
     /// Initial context-window identity captured when the thread was created.