diff --git a/codex-rs/config/src/loader/mod.rs b/codex-rs/config/src/loader/mod.rs
index 6e1dd082fa..2ab8e45c46 100644
--- a/codex-rs/config/src/loader/mod.rs
+++ b/codex-rs/config/src/loader/mod.rs
@@ -506,6 +506,21 @@ pub async fn load_config_layers_state(
                 ignore_user_and_project_exec_policy_rules,
             );
     config_layer_stack.is_projectless = is_projectless;
+    if config_layer_stack.layers_low_to_high().any(|layer| {
+        matches!(
+            layer.name,
+            ConfigLayerSource::User { .. } | ConfigLayerSource::Project { .. }
+        ) && layer
+            .config
+            .get("features")
+            .and_then(|features| features.get("multi_agent"))
+            .and_then(TomlValue::as_bool)
+            .is_some()
+    }) {
+        startup_warnings.push(
+            "`[features].multi_agent` is deprecated. It still controls the V1 fallback. `[agents].enabled = false` disables subagent tools even when the model selects a subagent version, unless `[features].multi_agent_v2` is enabled.".to_string(),
+        );
+    }
     startup_warnings.extend(ignored_config_warning(
         &config_layer_stack,
         &requirements_layers,
diff --git a/codex-rs/config/src/loader/tests.rs b/codex-rs/config/src/loader/tests.rs
index e38074b812..840882ac43 100644
--- a/codex-rs/config/src/loader/tests.rs
+++ b/codex-rs/config/src/loader/tests.rs
@@ -718,6 +718,63 @@ async fn missing_packaged_defaults_file_returns_an_error() {
     );
 }
 
+#[tokio::test]
+async fn multi_agent_warns_for_explicit_user_and_project_settings() -> std::io::Result<()> {
+    let home = tempdir()?;
+    let workspace = tempdir()?;
+    let cwd = AbsolutePathBuf::try_from(workspace.path())?;
+    let trust_key = TomlValue::String(project_trust_key(workspace.path()));
+    let project_config_dir = workspace.path().join(".codex");
+    std::fs::create_dir(&project_config_dir)?;
+    let session_flags = [(
+        "features.multi_agent".to_string(),
+        TomlValue::Boolean(false),
+    )];
+    for (user, project, flags, warn) in [
+        ("", "", session_flags.as_slice(), false),
+        ("[features]\nmulti_agent = false", "", &[], true),
+        (
+            "",
+            "[features]\nmulti_agent = true",
+            session_flags.as_slice(),
+            true,
+        ),
+    ] {
+        std::fs::write(
+            home.path().join(CONFIG_TOML_FILE),
+            format!("[projects.{trust_key}]\ntrust_level = 'trusted'\n{user}"),
+        )?;
+        std::fs::write(project_config_dir.join(CONFIG_TOML_FILE), project)?;
+        let stack = load_config_layers_state(
+            &TestFileSystem,
+            home.path(),
+            Some(cwd.clone()),
+            flags,
+            LoaderOverrides::without_managed_config_for_tests(),
+            &crate::NoopThreadConfigLoader,
+        )
+        .await?;
+        let warned = stack
+            .startup_warnings()
+            .unwrap_or_default()
+            .iter()
+            .any(|warning| {
+                warning.contains(
+                    "`[features].multi_agent` is deprecated. It still controls the V1 fallback.",
+                )
+            });
+        assert_eq!(
+            (
+                stack.effective_config()["features"]["multi_agent"].as_bool(),
+                warned
+            ),
+            (Some(false), warn),
+            "user={user:?}, project={project:?}"
+        );
+    }
+    Ok(())
+}
+
 #[cfg(windows)]
 #[tokio::test]
 async fn default_windows_managed_config_is_ignored_with_warning() {
diff --git a/codex-rs/features/src/lib.rs b/codex-rs/features/src/lib.rs
index f76315c675..65a43d8157 100644
--- a/codex-rs/features/src/lib.rs
+++ b/codex-rs/features/src/lib.rs
@@ -1630,7 +1630,7 @@ pub const FEATURES: &[FeatureSpec] = &[
     FeatureSpec {
         id: Feature::Collab,
         key: "multi_agent",
-        stage: Stage::Stable,
+        stage: Stage::Deprecated,
         default_enabled: true,
     },
     FeatureSpec {
diff --git a/codex-rs/features/src/tests.rs b/codex-rs/features/src/tests.rs
index 67d4e8b325..f841737d8e 100644
--- a/codex-rs/features/src/tests.rs
+++ b/codex-rs/features/src/tests.rs
@@ -142,13 +142,16 @@ fn codex_apps_mcp_protocol_can_be_enabled_independently_of_generic_mcp() {
 }
 
 #[test]
-fn default_enabled_features_are_stable() {
+fn default_enabled_features_have_shipped() {
     for spec in crate::FEATURES {
         // Instant interrupts are enabled by default while retaining their development stage.
         if spec.default_enabled && spec.id != Feature::InstantInterrupt {
             assert!(
-                matches!(spec.stage, Stage::Stable | Stage::Removed),
-                "feature `{}` is enabled by default but is not stable/removed ({:?})",
+                matches!(
+                    spec.stage,
+                    Stage::Stable | Stage::Deprecated | Stage::Removed
+                ),
+                "feature `{}` is enabled by default at stage {:?}",
                 spec.key,
                 spec.stage
             );