diff --git a/server/src/io/watcher.rs b/server/src/io/watcher.rs
index ced9b9e..54bf5cf 100644
--- a/server/src/io/watcher.rs
+++ b/server/src/io/watcher.rs
@@ -51,7 +51,19 @@ fn stage_metadata(stage: &str, item_id: &str) -> Option<(&'static str, String)>
 
 /// Return the pipeline stage name for a path if it is a `.md` file living
 /// directly inside one of the known work subdirectories, otherwise `None`.
+///
+/// Explicitly returns `None` for any path under `.story_kit/worktrees/` so
+/// that code changes made by agents in their isolated worktrees are never
+/// auto-committed to master by the watcher.
 fn stage_for_path(path: &Path) -> Option<String> {
+    // Reject any path that passes through the worktrees directory.
+    if path
+        .components()
+        .any(|c| c.as_os_str() == "worktrees")
+    {
+        return None;
+    }
+
     if path.extension().is_none_or(|e| e != "md") {
         return None;
     }
@@ -267,6 +279,31 @@ mod tests {
         );
     }
 
+    #[test]
+    fn stage_for_path_ignores_worktree_paths() {
+        let worktrees = PathBuf::from("/proj/.story_kit/worktrees");
+
+        // Code changes inside a worktree must be ignored.
+        assert_eq!(
+            stage_for_path(&worktrees.join("42_story_foo/server/src/main.rs")),
+            None,
+        );
+
+        // Even if a worktree happens to contain a path component that looks
+        // like a pipeline stage, it must still be ignored.
+        assert_eq!(
+            stage_for_path(&worktrees.join("42_story_foo/.story_kit/work/2_current/42_story_foo.md")),
+            None,
+        );
+
+        // A path that only contains the word "worktrees" as part of a longer
+        // segment (not an exact component) must NOT be filtered out.
+        assert_eq!(
+            stage_for_path(&PathBuf::from("/proj/.story_kit/work/2_current/not_worktrees_story.md")),
+            Some("2_current".to_string()),
+        );
+    }
+
     #[test]
     fn stage_metadata_returns_correct_actions() {
         let (action, msg) = stage_metadata("2_current", "42_story_foo").unwrap();