diff --git a/rust/rubydex-mcp/src/server.rs b/rust/rubydex-mcp/src/server.rs
index f40bc1637..deacacb93 100644
--- a/rust/rubydex-mcp/src/server.rs
+++ b/rust/rubydex-mcp/src/server.rs
@@ -20,6 +20,20 @@ use rubydex::model::{
 };
 use url::Url;
 
+/// Directory names that are never worth descending into while indexing a workspace.
+/// Mirrors `Rubydex::Graph::IGNORED_DIRECTORIES` in the Ruby gem.
+const IGNORED_DIRECTORIES: &[&str] = &[
+    ".bundle",
+    ".claude",
+    ".git",
+    ".github",
+    ".ruby-lsp",
+    ".vscode",
+    "log",
+    "node_modules",
+    "tmp",
+];
+
 struct ServerState {
     graph: Option<Graph>,
     error: Option<String>,
@@ -46,9 +60,10 @@ impl RubydexServer {
     /// Spawns a background thread that indexes the codebase and marks the server as ready.
     pub fn spawn_indexer(&self, path: String) {
         let state = Arc::clone(&self.state);
+        let excluded = default_excluded_paths(&path);
         std::thread::spawn(move || {
             let result = std::panic::catch_unwind(std::panic::AssertUnwindSafe(|| {
-                let (file_paths, errors) = rubydex::listing::collect_file_paths(vec![path], &HashSet::new());
+                let (file_paths, errors) = rubydex::listing::collect_file_paths(vec![path], &excluded);
                 for error in &errors {
                     eprintln!("Listing error: {error}");
                 }
@@ -95,6 +110,13 @@ impl RubydexServer {
     }
 }
 
+/// Builds the set of paths to skip during file discovery: each `IGNORED_DIRECTORIES`
+/// entry resolved against the workspace root.
+fn default_excluded_paths(root: &str) -> HashSet<PathBuf> {
+    let root = Path::new(root);
+    IGNORED_DIRECTORIES.iter().map(|dir| root.join(dir)).collect()
+}
+
 /// Returns a structured JSON error string with a machine-readable type, message, and suggestion.
 fn error_json(error_type: &str, message: &str, suggestion: &str) -> String {
     serde_json::to_string(&serde_json::json!({
@@ -1141,4 +1163,15 @@ mod tests {
         }
         assert_error(&server.codebase_stats(), "indexing_failed");
     }
+
+    #[test]
+    fn default_excluded_paths_resolves_ignored_dirs_against_root() {
+        let excluded = default_excluded_paths("/workspace");
+
+        assert_eq!(excluded.len(), IGNORED_DIRECTORIES.len());
+        assert!(excluded.contains(&PathBuf::from("/workspace/.claude")));
+        assert!(excluded.contains(&PathBuf::from("/workspace/node_modules")));
+        assert!(excluded.contains(&PathBuf::from("/workspace/tmp")));
+        assert!(!excluded.contains(&PathBuf::from("/workspace/lib")));
+    }
 }
diff --git a/rust/rubydex-mcp/tests/mcp.rs b/rust/rubydex-mcp/tests/mcp.rs
index cac8beb14..0611e2201 100644
--- a/rust/rubydex-mcp/tests/mcp.rs
+++ b/rust/rubydex-mcp/tests/mcp.rs
@@ -300,3 +300,58 @@ fn mcp_server_e2e() {
         let _ = child.wait().unwrap();
     });
 }
+
+#[test]
+fn mcp_server_skips_ignored_directories() {
+    with_context(|context| {
+        context.write("app.rb", "class IndexedClass; end");
+        // Lives under an ignored directory and must never be indexed.
+        context.write(".claude/worktrees/scratch.rb", "class IgnoredClass; end");
+
+        let mut child = Command::cargo_bin("rubydex_mcp")
+            .unwrap()
+            .args([context.absolute_path().to_str().unwrap()])
+            .stdin(Stdio::piped())
+            .stdout(Stdio::piped())
+            .stderr(Stdio::piped())
+            .spawn()
+            .unwrap();
+
+        let mut stdin = child.stdin.take().unwrap();
+        let stdout = child.stdout.take().unwrap();
+        let mut reader = BufReader::new(stdout);
+
+        initialize_session(&mut stdin, &mut reader);
+
+        let mut request_id = 3;
+        let stats = wait_for_indexing_to_complete(&mut stdin, &mut reader, &mut request_id);
+        // app.rb plus the synthetic core document; scratch.rb under .claude is excluded.
+        assert_eq!(stats["files"], 2, "Expected only app.rb to be indexed");
+
+        let search_response = call_next_tool(
+            &mut stdin,
+            &mut reader,
+            &mut request_id,
+            "search_declarations",
+            &json!({ "query": "IgnoredClass" }),
+        );
+        assert_eq!(
+            search_response["total"].as_u64().unwrap(),
+            0,
+            "Expected no results for a declaration under .claude, got: {search_response}"
+        );
+
+        let indexed_response = call_next_tool(
+            &mut stdin,
+            &mut reader,
+            &mut request_id,
+            "search_declarations",
+            &json!({ "query": "IndexedClass" }),
+        );
+        let indexed_names = names_from_entries(indexed_response["results"].as_array().unwrap());
+        assert_has_name(&indexed_names, "IndexedClass", "search results");
+
+        drop(stdin);
+        let _ = child.wait().unwrap();
+    });
+}