diff --git a/crates/oxc_language_server/src/backend.rs b/crates/oxc_language_server/src/backend.rs
index fc3f39f9d5eaa..2459c8a3f046c 100644
--- a/crates/oxc_language_server/src/backend.rs
+++ b/crates/oxc_language_server/src/backend.rs
@@ -13,7 +13,7 @@ use tower_lsp_server::{
         DidChangeWorkspaceFoldersParams, DidCloseTextDocumentParams, DidOpenTextDocumentParams,
         DidSaveTextDocumentParams, DocumentFormattingParams, ExecuteCommandParams,
         InitializeParams, InitializeResult, InitializedParams, Registration, ServerInfo, TextEdit,
-        Unregistration, Uri,
+        Uri,
     },
 };
 
@@ -218,7 +218,21 @@ impl LanguageServer for Backend {
     ///
     /// See: <https://microsoft.github.io/language-server-protocol/specifications/specification-current/#shutdown>
     async fn shutdown(&self) -> Result<()> {
-        self.clear_all_diagnostics().await;
+        let mut clearing_diagnostics = Vec::new();
+        let mut removed_registrations = Vec::new();
+
+        for worker in &*self.workspace_workers.read().await {
+            let (uris, unregistrations) = worker.shutdown().await;
+            clearing_diagnostics.extend(uris);
+            removed_registrations.extend(unregistrations);
+        }
+        self.clear_diagnostics(clearing_diagnostics).await;
+        if !removed_registrations.is_empty()
+            && let Err(err) = self.client.unregister_capability(removed_registrations).await
+        {
+            warn!("sending unregisterCapability.didChangeWatchedFiles failed: {err}");
+        }
+
         if self.capabilities.get().is_some_and(|option| option.dynamic_formatting) {
             self.file_system.write().await.clear();
         }
@@ -387,15 +401,13 @@ impl LanguageServer for Backend {
             else {
                 continue;
             };
-            cleared_diagnostics.extend(worker.get_clear_diagnostics().await);
-            removed_registrations.push(Unregistration {
-                id: format!("watcher-{}", worker.get_root_uri().as_str()),
-                method: "workspace/didChangeWatchedFiles".to_string(),
-            });
+            let (uris, unregistrations) = worker.shutdown().await;
+            cleared_diagnostics.extend(uris);
+            removed_registrations.extend(unregistrations);
             workers.remove(index);
         }
 
-        self.publish_all_diagnostics(&cleared_diagnostics).await;
+        self.clear_diagnostics(cleared_diagnostics).await;
 
         // client support `workspace/configuration` request
         if self.capabilities.get().is_some_and(|capabilities| capabilities.workspace_configuration)
@@ -632,14 +644,10 @@ impl Backend {
         configs
     }
 
-    /// Clears all diagnostics for workspace folders
-    async fn clear_all_diagnostics(&self) {
-        let mut cleared_diagnostics = vec![];
-        let workers = &*self.workspace_workers.read().await;
-        for worker in workers {
-            cleared_diagnostics.extend(worker.get_clear_diagnostics().await);
-        }
-        self.publish_all_diagnostics(&cleared_diagnostics).await;
+    async fn clear_diagnostics(&self, uris: Vec<Uri>) {
+        let diagnostics: Vec<(String, Vec<Diagnostic>)> =
+            uris.into_iter().map(|uri| (uri.to_string(), vec![])).collect();
+        self.publish_all_diagnostics(&diagnostics).await;
     }
 
     /// Publish diagnostics for all files.
diff --git a/crates/oxc_language_server/src/linter/server_linter.rs b/crates/oxc_language_server/src/linter/server_linter.rs
index 069c6d65ae858..4dc6742cccaac 100644
--- a/crates/oxc_language_server/src/linter/server_linter.rs
+++ b/crates/oxc_language_server/src/linter/server_linter.rs
@@ -19,7 +19,7 @@ use oxc_linter::{
     LintIgnoreMatcher, LintOptions, Oxlintrc,
 };
 
-use crate::tool::{Tool, ToolBuilder};
+use crate::tool::{Tool, ToolBuilder, ToolShutdownChanges};
 use crate::{
     ConcurrentHashMap,
     linter::{
@@ -245,6 +245,12 @@ pub struct ServerLinter {
 }
 
 impl Tool for ServerLinter {
+    fn shutdown(&self) -> ToolShutdownChanges {
+        ToolShutdownChanges {
+            uris_to_clear_diagnostics: Some(self.get_cached_files_of_diagnostics()),
+        }
+    }
+
     /// # Panics
     /// Panics if the root URI cannot be converted to a file path.
     async fn handle_configuration_change(
@@ -522,7 +528,7 @@ impl ServerLinter {
         None
     }
 
-    pub fn get_cached_files_of_diagnostics(&self) -> Vec<Uri> {
+    fn get_cached_files_of_diagnostics(&self) -> Vec<Uri> {
         self.diagnostics.pin().keys().filter_map(|s| Uri::from_str(s).ok()).collect()
     }
 
diff --git a/crates/oxc_language_server/src/tool.rs b/crates/oxc_language_server/src/tool.rs
index ca975837d1a85..8d272305c9bca 100644
--- a/crates/oxc_language_server/src/tool.rs
+++ b/crates/oxc_language_server/src/tool.rs
@@ -113,6 +113,11 @@ pub trait Tool: Sized {
     fn remove_diagnostics(&self, _uri: &Uri) {
         // Default implementation does nothing.
     }
+
+    /// Shutdown the tool and return any necessary changes to be made after shutdown.
+    fn shutdown(&self) -> ToolShutdownChanges {
+        ToolShutdownChanges { uris_to_clear_diagnostics: None }
+    }
 }
 
 pub struct ToolRestartChanges<T> {
@@ -125,3 +130,8 @@ pub struct ToolRestartChanges<T> {
     /// 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 34f117ff9f284..cdef4195d76a4 100644
--- a/crates/oxc_language_server/src/worker.rs
+++ b/crates/oxc_language_server/src/worker.rs
@@ -184,26 +184,31 @@ impl WorkspaceWorker {
         server_formatter.run_format(uri, content)
     }
 
-    /// Get all clear diagnostics for the current workspace
-    /// This should be called when:
-    /// - The linter is disabled (not currently implemented)
-    /// - The workspace is closed
-    /// - The server is shut down
-    ///
-    /// This will return a list of URIs that had diagnostics before, each with an empty diagnostics list
-    pub async fn get_clear_diagnostics(&self) -> Vec<(String, Vec<Diagnostic>)> {
-        self.server_linter
-            .read()
-            .await
-            .as_ref()
-            .map(|server_linter| {
-                server_linter
-                    .get_cached_files_of_diagnostics()
-                    .iter()
-                    .map(|uri| (uri.to_string(), vec![]))
-                    .collect::<Vec<_>>()
-            })
-            .unwrap_or_default()
+    /// Shutdown the worker and return any necessary changes to be made after shutdown.
+    /// This includes clearing diagnostics and unregistering file watchers.
+    pub async fn shutdown(
+        &self,
+    ) -> (
+        // 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();
+
+        if let Some(server_linter) = &*self.server_linter.read().await
+            && let Some(uris) = server_linter.shutdown().uris_to_clear_diagnostics
+        {
+            uris_to_clear_diagnostics.extend(uris);
+        }
+
+        (
+            uris_to_clear_diagnostics,
+            vec![
+                unregistration_tool_watcher_id("linter", &self.root_uri),
+                unregistration_tool_watcher_id("formatter", &self.root_uri),
+            ],
+        )
     }
 
     /// Get code actions or commands for the given range