diff --git a/crates/tui/src/runtime_api.rs b/crates/tui/src/runtime_api.rs
index 553d308a..3b2de2f6 100644
--- a/crates/tui/src/runtime_api.rs
+++ b/crates/tui/src/runtime_api.rs
@@ -961,9 +961,8 @@ async fn list_skills(
     State(state): State<RuntimeApiState>,
 ) -> Result<Json<SkillsResponse>, ApiError> {
     let skills_dir = resolve_skills_dir(&state.config, &state.workspace);
-    let registry = crate::skills::discover_for_workspace_and_dir(&state.workspace, &skills_dir);
+    let (registry, directories) = discover_skills_for_runtime_api(&state.workspace, &skills_dir);
     let skill_state = state.skill_state.lock().await;
-    let directories = skills_search_directories(&state.workspace, &skills_dir);
     let skills = registry
         .list()
         .iter()
@@ -972,7 +971,7 @@ async fn list_skills(
             description: skill.description.clone(),
             path: skill.path.clone(),
             enabled: skill_state.is_enabled(&skill.name),
-            is_bundled: crate::skills::is_bundled_skill_name(&skill.name),
+            is_bundled: skill_entry_is_bundled(skill, &skills_dir),
         })
         .collect();
     Ok(Json(SkillsResponse {
@@ -989,12 +988,12 @@ async fn set_skill_enabled(
     Json(req): Json<SetSkillEnabledRequest>,
 ) -> Result<Json<SetSkillEnabledResponse>, ApiError> {
     let skills_dir = resolve_skills_dir(&state.config, &state.workspace);
-    let registry = crate::skills::discover_for_workspace_and_dir(&state.workspace, &skills_dir);
+    let (registry, directories) = discover_skills_for_runtime_api(&state.workspace, &skills_dir);
     let exists = registry.list().iter().any(|skill| skill.name == name);
     if !exists {
         return Err(ApiError::not_found(format!(
             "skill '{name}' not found in searched directories: {}",
-            format_skill_search_paths(&skills_search_directories(&state.workspace, &skills_dir))
+            format_skill_search_paths(&directories)
         )));
     }
 
@@ -1778,6 +1777,31 @@ fn skills_search_directories(workspace: &FsPath, skills_dir: &FsPath) -> Vec<Pat
     directories
 }
 
+fn discover_skills_for_runtime_api(
+    workspace: &FsPath,
+    skills_dir: &FsPath,
+) -> (crate::skills::SkillRegistry, Vec<PathBuf>) {
+    let directories = skills_search_directories(workspace, skills_dir);
+    let registry = crate::skills::discover_from_directories(directories.clone());
+    (registry, directories)
+}
+
+fn skill_entry_is_bundled(skill: &crate::skills::Skill, skills_dir: &FsPath) -> bool {
+    if !crate::skills::is_bundled_skill_name(&skill.name) {
+        return false;
+    }
+
+    let expected_path = skills_dir.join(&skill.name).join("SKILL.md");
+    paths_refer_to_same_file(&skill.path, &expected_path)
+}
+
+fn paths_refer_to_same_file(left: &FsPath, right: &FsPath) -> bool {
+    match (fs::canonicalize(left), fs::canonicalize(right)) {
+        (Ok(left), Ok(right)) => left == right,
+        _ => left == right,
+    }
+}
+
 fn format_skill_search_paths(directories: &[PathBuf]) -> String {
     if directories.is_empty() {
         return "<none>".to_string();
@@ -3926,6 +3950,53 @@ mod tests {
         assert!(message.contains("custom-skills"));
     }
 
+    #[test]
+    fn skill_entry_is_bundled_requires_configured_bundle_path() {
+        let tmp = tempfile::tempdir().expect("tempdir");
+        let bundled_skills_dir = tmp.path().join("bundled-skills");
+        let bundled_skill_path = bundled_skills_dir.join("delegate").join("SKILL.md");
+        let override_skill_path = tmp
+            .path()
+            .join("workspace")
+            .join(".agents")
+            .join("skills")
+            .join("delegate")
+            .join("SKILL.md");
+        fs::create_dir_all(bundled_skill_path.parent().expect("bundled parent"))
+            .expect("create bundled skill dir");
+        fs::create_dir_all(override_skill_path.parent().expect("override parent"))
+            .expect("create override skill dir");
+        fs::write(
+            &bundled_skill_path,
+            "---\nname: delegate\ndescription: bundled\n---\n",
+        )
+        .expect("write bundled skill");
+        fs::write(
+            &override_skill_path,
+            "---\nname: delegate\ndescription: override\n---\n",
+        )
+        .expect("write override skill");
+
+        let bundled_skill = crate::skills::Skill {
+            name: "delegate".to_string(),
+            description: String::new(),
+            body: String::new(),
+            path: bundled_skill_path,
+        };
+        let override_skill = crate::skills::Skill {
+            name: "delegate".to_string(),
+            description: String::new(),
+            body: String::new(),
+            path: override_skill_path,
+        };
+
+        assert!(skill_entry_is_bundled(&bundled_skill, &bundled_skills_dir));
+        assert!(!skill_entry_is_bundled(
+            &override_skill,
+            &bundled_skills_dir
+        ));
+    }
+
     /// A `skills` symlink that points outside the workspace must NOT be
     /// returned as the resolved skills directory. Containment check ensures
     /// the canonicalized candidate stays under the canonicalized workspace
diff --git a/crates/tui/src/skills/mod.rs b/crates/tui/src/skills/mod.rs
index d962d32e..d2c2f6ad 100644
--- a/crates/tui/src/skills/mod.rs
+++ b/crates/tui/src/skills/mod.rs
@@ -580,6 +580,10 @@ fn discover_for_workspace_dirs_and_dir(mut dirs: Vec<PathBuf>, skills_dir: &Path
         dirs.push(skills_dir.to_path_buf());
     }
 
+    discover_from_directories(dirs)
+}
+
+pub(crate) fn discover_from_directories(dirs: impl IntoIterator<Item = PathBuf>) -> SkillRegistry {
     let mut merged = SkillRegistry::default();
     for dir in dirs {
         let registry = SkillRegistry::discover(&dir);