diff --git a/server/src/worktree.rs b/server/src/worktree.rs
index 52147c5..4348c0a 100644
--- a/server/src/worktree.rs
+++ b/server/src/worktree.rs
@@ -253,7 +253,23 @@ fn remove_worktree_sync(project_root: &Path, wt_path: &Path, branch: &str) -> Re
 
     if !output.status.success() {
         let stderr = String::from_utf8_lossy(&output.stderr);
-        slog!("[worktree] remove warning: {stderr}");
+        if stderr.contains("not a working tree") {
+            // Orphaned directory: git doesn't recognise it as a worktree.
+            // Remove the directory directly and prune stale git metadata.
+            slog!(
+                "[worktree] orphaned worktree detected, removing directory: {}",
+                wt_path.display()
+            );
+            if let Err(e) = std::fs::remove_dir_all(wt_path) {
+                slog!("[worktree] failed to remove orphaned directory: {e}");
+            }
+            let _ = Command::new("git")
+                .args(["worktree", "prune"])
+                .current_dir(project_root)
+                .output();
+        } else {
+            slog!("[worktree] remove warning: {stderr}");
+        }
     }
 
     // Delete branch (best effort)
@@ -630,6 +646,28 @@ mod tests {
         );
     }
 
+    #[test]
+    fn remove_worktree_sync_removes_orphaned_directory() {
+        let tmp = TempDir::new().unwrap();
+        let project_root = tmp.path().join("my-project");
+        fs::create_dir_all(&project_root).unwrap();
+        init_git_repo(&project_root);
+
+        // Create a directory that looks like a worktree but isn't registered with git
+        let wt_path = project_root
+            .join(".storkit")
+            .join("worktrees")
+            .join("orphan");
+        fs::create_dir_all(&wt_path).unwrap();
+        fs::write(wt_path.join("some_file.txt"), "stale").unwrap();
+        assert!(wt_path.exists());
+
+        // git worktree remove will fail with "not a working tree",
+        // but the fallback should rm -rf the directory
+        remove_worktree_sync(&project_root, &wt_path, "feature/orphan").unwrap();
+        assert!(!wt_path.exists());
+    }
+
     #[test]
     fn remove_worktree_sync_cleans_up_directory() {
         let tmp = TempDir::new().unwrap();