diff --git a/server/src/worktree.rs b/server/src/worktree.rs
index b622d2f..3dc024e 100644
--- a/server/src/worktree.rs
+++ b/server/src/worktree.rs
@@ -161,9 +161,18 @@ fn create_worktree_sync(
 /// from being committed on feature branches, which avoids rename/delete merge
 /// conflicts when merging back to master.
 fn configure_sparse_checkout(wt_path: &Path) -> Result<(), String> {
-    // Enable sparse checkout via git config (non-cone mode for pattern support)
+    // Enable worktree-specific config so sparse checkout settings don't leak
+    // to the main checkout or other worktrees.
+    let _ = Command::new("git")
+        .args(["config", "extensions.worktreeConfig", "true"])
+        .current_dir(wt_path)
+        .output();
+
+    // Enable sparse checkout for THIS worktree only (--worktree flag).
+    // Without --worktree, this writes to the shared .git/config and
+    // enables sparse checkout on the main checkout too.
     let output = Command::new("git")
-        .args(["config", "core.sparseCheckout", "true"])
+        .args(["config", "--worktree", "core.sparseCheckout", "true"])
         .current_dir(wt_path)
         .output()
         .map_err(|e| format!("sparse-checkout config: {e}"))?;
@@ -475,5 +484,12 @@ mod tests {
 
         // Other files should still exist
         assert!(wt_path.join(".git").exists());
+
+        // Main checkout must NOT be affected by the worktree's sparse checkout.
+        // The .story_kit/work/ directory must still exist in the project root.
+        assert!(
+            work_dir.exists(),
+            ".story_kit/work/ must still exist in the main checkout"
+        );
     }
 }