diff --git a/apps/oxlint/src/js_plugins/external_linter.rs b/apps/oxlint/src/js_plugins/external_linter.rs
index 4d241302d47d4..b49a919b7c7de 100644
--- a/apps/oxlint/src/js_plugins/external_linter.rs
+++ b/apps/oxlint/src/js_plugins/external_linter.rs
@@ -1,4 +1,7 @@
-use std::sync::{Arc, atomic::Ordering, mpsc::channel};
+use std::{
+    sync::{Arc, atomic::Ordering, mpsc::channel},
+    time::Duration,
+};
 
 use napi::{
     Status,
@@ -326,8 +329,40 @@ fn wrap_create_workspace(cb: JsCreateWorkspaceCb) -> ExternalLinterCreateWorkspa
 }
 
 /// Wrap `destroyWorkspace` JS callback as a normal Rust function.
+///
+/// The JS-side `destroyWorkspace` function is synchronous, but it's wrapped in a `ThreadsafeFunction`,
+/// so cannot be called synchronously. Use an `mpsc::channel` to wait for the result from JS side.
+///
+/// Uses a timeout to prevent indefinite blocking during shutdown, which can cause issues
+/// in multi-root workspace scenarios where multiple workspaces are being destroyed concurrently.
 fn wrap_destroy_workspace(cb: JsDestroyWorkspaceCb) -> ExternalLinterDestroyWorkspaceCb {
     Arc::new(Box::new(move |workspace_uri| {
-        let _ = cb.call(workspace_uri, ThreadsafeFunctionCallMode::NonBlocking);
+        let (tx, rx) = channel();
+
+        // Send data to JS
+        let status = cb.call_with_return_value(
+            workspace_uri,
+            ThreadsafeFunctionCallMode::NonBlocking,
+            move |result, _env| {
+                // Ignore send errors - the receiver may have timed out
+                let _ = tx.send(result);
+                Ok(())
+            },
+        );
+
+        if status == Status::Ok {
+            // Use a timeout to prevent blocking indefinitely during shutdown.
+            // If JS side doesn't respond within the timeout, we proceed with shutdown anyway.
+            match rx.recv_timeout(Duration::from_secs(5)) {
+                // Destroying workspace succeeded
+                Ok(Ok(()))
+                // Timeout or sender dropped - proceed with shutdown
+                | Err(_) => Ok(()),
+                // `destroyWorkspace` threw an error
+                Ok(Err(err)) => Err(format!("`destroyWorkspace` threw an error: {err}")),
+            }
+        } else {
+            Err(format!("Failed to schedule `destroyWorkspace` callback: {status:?}"))
+        }
     }))
 }
diff --git a/apps/oxlint/src/lsp/server_linter.rs b/apps/oxlint/src/lsp/server_linter.rs
index 7da9b9d752438..786fbbcd7f0ff 100644
--- a/apps/oxlint/src/lsp/server_linter.rs
+++ b/apps/oxlint/src/lsp/server_linter.rs
@@ -301,7 +301,11 @@ impl ToolBuilder for ServerLinterBuilder {
     fn shutdown(&self, root_uri: &Uri) {
         // Destroy JS workspace
         if let Some(external_linter) = &self.external_linter {
-            (external_linter.destroy_workspace)(root_uri.as_str().to_string());
+            let res = (external_linter.destroy_workspace)(root_uri.as_str().to_string());
+
+            if let Err(err) = res {
+                error!("Failed to destroy JS workspace:\n{err}\n");
+            }
         }
     }
 }
diff --git a/crates/oxc_linter/src/external_linter.rs b/crates/oxc_linter/src/external_linter.rs
index ba9f62b42be0c..e87d31ab27258 100644
--- a/crates/oxc_linter/src/external_linter.rs
+++ b/crates/oxc_linter/src/external_linter.rs
@@ -12,7 +12,8 @@ use crate::{
 pub type ExternalLinterCreateWorkspaceCb =
     Arc<Box<dyn Fn(String) -> Result<(), String> + Send + Sync>>;
 
-pub type ExternalLinterDestroyWorkspaceCb = Arc<Box<dyn Fn(String) + Send + Sync>>;
+pub type ExternalLinterDestroyWorkspaceCb =
+    Arc<Box<dyn Fn(String) -> Result<(), String> + Send + Sync>>;
 
 pub type ExternalLinterLoadPluginCb = Arc<
     Box<