diff --git a/crates/oxc_language_server/src/backend.rs b/crates/oxc_language_server/src/backend.rs
index c1a2f762fce6f..43689fc6a3872 100644
--- a/crates/oxc_language_server/src/backend.rs
+++ b/crates/oxc_language_server/src/backend.rs
@@ -251,7 +251,7 @@ impl LanguageServer for Backend {
         let mut removed_registrations = Vec::new();
 
         for worker in &*self.workspace_workers.read().await {
-            let (uris, unregistrations) = worker.shutdown().await;
+            let (uris, unregistrations) = worker.shutdown(&*self.file_system.read().await).await;
             clearing_diagnostics.extend(uris);
             removed_registrations.extend(unregistrations);
         }
@@ -439,7 +439,7 @@ impl LanguageServer for Backend {
             else {
                 continue;
             };
-            let (uris, unregistrations) = worker.shutdown().await;
+            let (uris, unregistrations) = worker.shutdown(&*self.file_system.read().await).await;
             cleared_diagnostics.extend(uris);
             removed_registrations.extend(unregistrations);
             workers.remove(index);
diff --git a/crates/oxc_language_server/src/lib.rs b/crates/oxc_language_server/src/lib.rs
index ba1ef900a7339..7d6065ba24dae 100644
--- a/crates/oxc_language_server/src/lib.rs
+++ b/crates/oxc_language_server/src/lib.rs
@@ -20,7 +20,7 @@ use crate::backend::Backend;
 pub use crate::formatter::ServerFormatterBuilder;
 #[cfg(feature = "linter")]
 pub use crate::linter::ServerLinterBuilder;
-pub use crate::tool::{Tool, ToolBuilder, ToolRestartChanges, ToolShutdownChanges};
+pub use crate::tool::{Tool, ToolBuilder, ToolRestartChanges};
 
 pub type ConcurrentHashMap<K, V> = papaya::HashMap<K, V, FxBuildHasher>;
 
diff --git a/crates/oxc_language_server/src/linter/server_linter.rs b/crates/oxc_language_server/src/linter/server_linter.rs
index 23f64e0611144..7c927c377d728 100644
--- a/crates/oxc_language_server/src/linter/server_linter.rs
+++ b/crates/oxc_language_server/src/linter/server_linter.rs
@@ -34,7 +34,7 @@ use crate::{
         isolated_lint_handler::{IsolatedLintHandler, IsolatedLintHandlerOptions},
         options::{LintOptions as LSPLintOptions, Run, UnusedDisableDirectives},
     },
-    tool::{Tool, ToolBuilder, ToolRestartChanges, ToolShutdownChanges},
+    tool::{Tool, ToolBuilder, ToolRestartChanges},
     utils::normalize_path,
 };
 
@@ -310,10 +310,6 @@ impl Tool for ServerLinter {
         "linter"
     }
 
-    fn shutdown(&self) -> ToolShutdownChanges {
-        ToolShutdownChanges { uris_to_clear_diagnostics: Some(self.get_cached_uris()) }
-    }
-
     /// # Panics
     /// Panics if the root URI cannot be converted to a file path.
     fn handle_configuration_change(
@@ -552,10 +548,6 @@ impl ServerLinter {
         }
     }
 
-    fn get_cached_uris(&self) -> Vec<Uri> {
-        self.code_actions.pin().keys().cloned().collect()
-    }
-
     fn get_code_actions_for_uri(&self, uri: &Uri) -> Option<Vec<LinterCodeAction>> {
         if let Some(cached_code_actions) = self.code_actions.pin().get(uri) {
             cached_code_actions.clone()
diff --git a/crates/oxc_language_server/src/tests.rs b/crates/oxc_language_server/src/tests.rs
index 267093db58b3d..0a741994999be 100644
--- a/crates/oxc_language_server/src/tests.rs
+++ b/crates/oxc_language_server/src/tests.rs
@@ -280,6 +280,20 @@ impl TestServer {
         assert_eq!(shutdown_result.id(), &Id::Number(id));
     }
 
+    async fn shutdown_with_diagnostics_clear(&mut self, id: i64) {
+        // shutdown request
+        self.send_request(shutdown_request(id)).await;
+
+        // diagnostics clear expected
+        acknowledge_publish_diagnostics(self).await;
+
+        // shutdown response
+        let shutdown_result = self.recv_response().await;
+
+        assert!(shutdown_result.is_ok());
+        assert_eq!(shutdown_result.id(), &Id::Number(id));
+    }
+
     async fn shutdown_with_watchers(&mut self, id: i64) {
         // shutdown request
         self.send_request(shutdown_request(id)).await;
@@ -375,6 +389,16 @@ async fn acknowledge_unregistrations(server: &mut TestServer) {
     server.send_ack(unregister_request.id().unwrap()).await;
 }
 
+async fn acknowledge_publish_diagnostics(server: &mut TestServer) {
+    let diagnostic_request = server.recv_notification().await;
+    assert_eq!(diagnostic_request.method(), "textDocument/publishDiagnostics");
+
+    if let Some(id) = diagnostic_request.id() {
+        // Acknowledge the diagnostics
+        server.send_ack(id).await;
+    }
+}
+
 async fn response_to_configuration(
     server: &mut TestServer,
     configurations: Vec<serde_json::Value>,
@@ -481,11 +505,12 @@ mod test_suite {
     use crate::{
         backend::Backend,
         tests::{
-            FAKE_COMMAND, FakeToolBuilder, TestServer, WORKSPACE, acknowledge_registrations,
-            acknowledge_unregistrations, code_action, did_change, did_change_configuration,
-            did_change_watched_files, did_close, did_open, did_save, execute_command_request,
-            initialize_request, initialized_notification, response_to_configuration,
-            shutdown_request, test_configuration_request, workspace_folders_changed,
+            FAKE_COMMAND, FakeToolBuilder, TestServer, WORKSPACE, acknowledge_publish_diagnostics,
+            acknowledge_registrations, acknowledge_unregistrations, code_action, did_change,
+            did_change_configuration, did_change_watched_files, did_close, did_open, did_save,
+            execute_command_request, initialize_request, initialized_notification,
+            response_to_configuration, shutdown_request, test_configuration_request,
+            workspace_folders_changed,
         },
     };
 
@@ -1051,7 +1076,7 @@ mod test_suite {
         assert!(response.id() == &Id::Number(3));
         assert!(response.result().is_some_and(|result| *result == Value::Null));
 
-        server.shutdown(4).await;
+        server.shutdown_with_diagnostics_clear(4).await;
     }
 
     #[tokio::test]
@@ -1076,7 +1101,7 @@ mod test_suite {
         assert_eq!(actions.len(), 1);
         assert_eq!(actions[0]["title"], "Code Action title");
 
-        server.shutdown(4).await;
+        server.shutdown_with_diagnostics_clear(4).await;
     }
 
     #[tokio::test]
@@ -1102,7 +1127,12 @@ mod test_suite {
             format!("Fake diagnostic for content: {content}")
         );
 
-        server.shutdown(4).await;
+        if let Some(id) = diagnostic_response.id() {
+            // Acknowledge the diagnostics
+            server.send_ack(id).await;
+        }
+
+        server.shutdown_with_diagnostics_clear(4).await;
     }
 
     #[tokio::test]
@@ -1116,8 +1146,8 @@ mod test_suite {
         let file = format!("{WORKSPACE}/diagnostics.config");
         let content = "new text";
         server.send_request(did_open(&file, "old text")).await;
-        let diagnostic_response = server.recv_notification().await;
-        assert_eq!(diagnostic_response.method(), "textDocument/publishDiagnostics");
+
+        acknowledge_publish_diagnostics(&mut server).await;
 
         server.send_request(did_change(&file, content)).await;
 
@@ -1132,7 +1162,12 @@ mod test_suite {
             format!("Fake diagnostic for content: {content}")
         );
 
-        server.shutdown(4).await;
+        if let Some(id) = diagnostic_response.id() {
+            // Acknowledge the diagnostics
+            server.send_ack(id).await;
+        }
+
+        server.shutdown_with_diagnostics_clear(4).await;
     }
 
     #[tokio::test]
@@ -1146,13 +1181,11 @@ mod test_suite {
         let file = format!("{WORKSPACE}/diagnostics.config");
         let content = "new text";
         server.send_request(did_open(&file, "old text")).await;
-        let diagnostic_response = server.recv_notification().await;
-        assert_eq!(diagnostic_response.method(), "textDocument/publishDiagnostics");
+        acknowledge_publish_diagnostics(&mut server).await;
 
         server.send_request(did_change(&file, content)).await;
 
-        let diagnostic_response = server.recv_notification().await;
-        assert_eq!(diagnostic_response.method(), "textDocument/publishDiagnostics");
+        acknowledge_publish_diagnostics(&mut server).await;
 
         server.send_request(did_save(&file, content)).await;
 
@@ -1167,6 +1200,11 @@ mod test_suite {
             format!("Fake diagnostic for content: {content}")
         );
 
-        server.shutdown(4).await;
+        if let Some(id) = diagnostic_response.id() {
+            // Acknowledge the diagnostics
+            server.send_ack(id).await;
+        }
+
+        server.shutdown_with_diagnostics_clear(4).await;
     }
 }
diff --git a/crates/oxc_language_server/src/tool.rs b/crates/oxc_language_server/src/tool.rs
index 5667320e4546d..d7695257b268f 100644
--- a/crates/oxc_language_server/src/tool.rs
+++ b/crates/oxc_language_server/src/tool.rs
@@ -120,8 +120,8 @@ pub trait Tool: Send + Sync {
     }
 
     /// Shutdown the tool and return any necessary changes to be made after shutdown.
-    fn shutdown(&self) -> ToolShutdownChanges {
-        ToolShutdownChanges { uris_to_clear_diagnostics: None }
+    fn shutdown(&self) {
+        // Default implementation does nothing.
     }
 }
 
@@ -133,8 +133,3 @@ pub struct ToolRestartChanges {
     /// Old patterns will be automatically unregistered
     pub watch_patterns: Option<Vec<Pattern>>,
 }
-
-pub struct ToolShutdownChanges {
-    /// The URIs that need to have their diagnostics removed after the tool shutdown
-    pub uris_to_clear_diagnostics: Option<Vec<Uri>>,
-}
diff --git a/crates/oxc_language_server/src/worker.rs b/crates/oxc_language_server/src/worker.rs
index fc9ebaa97d40f..02595324780a7 100644
--- a/crates/oxc_language_server/src/worker.rs
+++ b/crates/oxc_language_server/src/worker.rs
@@ -168,24 +168,25 @@ impl WorkspaceWorker {
     /// This includes clearing diagnostics and unregistering file watchers.
     pub async fn shutdown(
         &self,
+        fs: &LSPFileSystem,
     ) -> (
         // The URIs that need to have their diagnostics removed after shutdown
         Vec<Uri>,
         // Watchers that need to be unregistered
         Vec<Unregistration>,
     ) {
-        let mut uris_to_clear_diagnostics = Vec::new();
         let mut watchers_to_unregister = Vec::new();
         for tool in self.tools.read().await.iter() {
-            let shutdown_changes = tool.shutdown();
-            if let Some(uris) = shutdown_changes.uris_to_clear_diagnostics {
-                uris_to_clear_diagnostics.extend(uris);
-            }
+            tool.shutdown();
+
             watchers_to_unregister
                 .push(unregistration_tool_watcher_id(tool.name(), &self.root_uri));
         }
 
-        (uris_to_clear_diagnostics, watchers_to_unregister)
+        (
+            fs.keys().into_iter().filter(|uri| self.is_responsible_for_uri(uri)).collect(),
+            watchers_to_unregister,
+        )
     }
 
     /// Get code actions or commands for the given range.