diff --git a/codex-rs/app-server/src/attestation.rs b/codex-rs/app-server/src/attestation.rs
index 17bb10c38c76..206c38cee17e 100644
--- a/codex-rs/app-server/src/attestation.rs
+++ b/codex-rs/app-server/src/attestation.rs
@@ -1,4 +1,5 @@
 use std::sync::Arc;
+use std::sync::Weak;
 
 use axum::http::HeaderValue;
 use codex_app_server_protocol::AttestationGenerateParams;
@@ -22,13 +23,13 @@ pub(crate) fn app_server_attestation_provider(
     thread_state_manager: ThreadStateManager,
 ) -> Arc<dyn AttestationProvider> {
     Arc::new(AppServerAttestationProvider {
-        outgoing,
+        outgoing: Arc::downgrade(&outgoing),
         thread_state_manager,
     })
 }
 
 struct AppServerAttestationProvider {
-    outgoing: Arc<OutgoingMessageSender>,
+    outgoing: Weak<OutgoingMessageSender>,
     thread_state_manager: ThreadStateManager,
 }
 
@@ -42,7 +43,9 @@ impl std::fmt::Debug for AppServerAttestationProvider {
 
 impl AttestationProvider for AppServerAttestationProvider {
     fn header_for_request(&self, context: AttestationContext) -> GenerateAttestationFuture<'_> {
-        let outgoing = self.outgoing.clone();
+        let Some(outgoing) = self.outgoing.upgrade() else {
+            return Box::pin(async { None });
+        };
         let thread_state_manager = self.thread_state_manager.clone();
         Box::pin(async move {
             request_attestation_header_value_with_timeout(
diff --git a/codex-rs/app-server/src/message_processor.rs b/codex-rs/app-server/src/message_processor.rs
index fdcd44d01aea..4b630d2ac37b 100644
--- a/codex-rs/app-server/src/message_processor.rs
+++ b/codex-rs/app-server/src/message_processor.rs
@@ -86,6 +86,7 @@ use tokio::sync::broadcast;
 use tokio::sync::watch;
 use tokio::time::Duration;
 use tokio::time::timeout;
+use tokio_util::sync::CancellationToken;
 use tracing::Instrument;
 
 const EXTERNAL_AUTH_REFRESH_TIMEOUT: Duration = Duration::from_secs(10);
@@ -160,6 +161,7 @@ impl ExternalAuth for ExternalAuthRefreshBridge {
 
 pub(crate) struct MessageProcessor {
     outgoing: Arc<OutgoingMessageSender>,
+    skills_watcher: Arc<SkillsWatcher>,
     account_processor: AccountRequestProcessor,
     apps_processor: AppsRequestProcessor,
     catalog_processor: CatalogRequestProcessor,
@@ -349,6 +351,7 @@ impl MessageProcessor {
         let thread_list_state_permit = Arc::new(Semaphore::new(/*permits*/ 1));
         let workspace_settings_cache =
             Arc::new(workspace_settings::WorkspaceSettingsCache::default());
+        let app_list_shutdown_token = CancellationToken::new();
         let account_processor = AccountRequestProcessor::new(
             auth_manager.clone(),
             Arc::clone(&thread_manager),
@@ -362,6 +365,7 @@ impl MessageProcessor {
             outgoing.clone(),
             config_manager.clone(),
             Arc::clone(&workspace_settings_cache),
+            app_list_shutdown_token,
         );
         let catalog_processor = CatalogRequestProcessor::new(
             auth_manager.clone(),
@@ -499,6 +503,7 @@ impl MessageProcessor {
 
         Self {
             outgoing,
+            skills_watcher,
             account_processor,
             apps_processor,
             catalog_processor,
@@ -527,6 +532,8 @@ impl MessageProcessor {
 
     pub(crate) fn clear_runtime_references(&self) {
         self.account_processor.clear_external_auth();
+        self.apps_processor.shutdown();
+        self.skills_watcher.shutdown();
     }
 
     pub(crate) async fn process_request(
diff --git a/codex-rs/app-server/src/request_processors.rs b/codex-rs/app-server/src/request_processors.rs
index 3e84c397f833..1dd8684ea6f9 100644
--- a/codex-rs/app-server/src/request_processors.rs
+++ b/codex-rs/app-server/src/request_processors.rs
@@ -423,6 +423,7 @@ use tokio::sync::broadcast;
 use tokio::sync::oneshot;
 use tokio::sync::watch;
 use tokio_util::sync::CancellationToken;
+use tokio_util::sync::DropGuard;
 use tokio_util::task::TaskTracker;
 use toml::Value as TomlValue;
 use tracing::Instrument;
diff --git a/codex-rs/app-server/src/request_processors/apps_processor.rs b/codex-rs/app-server/src/request_processors/apps_processor.rs
index caf60a91a014..5a1c9ffe1c4e 100644
--- a/codex-rs/app-server/src/request_processors/apps_processor.rs
+++ b/codex-rs/app-server/src/request_processors/apps_processor.rs
@@ -1,12 +1,13 @@
 use super::*;
 
-#[derive(Clone)]
 pub(crate) struct AppsRequestProcessor {
     auth_manager: Arc<AuthManager>,
     thread_manager: Arc<ThreadManager>,
     outgoing: Arc<OutgoingMessageSender>,
     config_manager: ConfigManager,
     workspace_settings_cache: Arc<workspace_settings::WorkspaceSettingsCache>,
+    shutdown_token: CancellationToken,
+    _shutdown_drop_guard: DropGuard,
 }
 
 impl AppsRequestProcessor {
@@ -16,13 +17,17 @@ impl AppsRequestProcessor {
         outgoing: Arc<OutgoingMessageSender>,
         config_manager: ConfigManager,
         workspace_settings_cache: Arc<workspace_settings::WorkspaceSettingsCache>,
+        shutdown_token: CancellationToken,
     ) -> Self {
+        let shutdown_drop_guard = shutdown_token.clone().drop_guard();
         Self {
             auth_manager,
             thread_manager,
             outgoing,
             config_manager,
             workspace_settings_cache,
+            shutdown_token,
+            _shutdown_drop_guard: shutdown_drop_guard,
         }
     }
 
@@ -83,12 +88,20 @@ impl AppsRequestProcessor {
         let request = request_id.clone();
         let outgoing = Arc::clone(&self.outgoing);
         let environment_manager = self.thread_manager.environment_manager();
+        let shutdown_token = self.shutdown_token.child_token();
         tokio::spawn(async move {
-            Self::apps_list_task(outgoing, request, params, config, environment_manager).await;
+            tokio::select! {
+                _ = shutdown_token.cancelled() => {}
+                _ = Self::apps_list_task(outgoing, request, params, config, environment_manager) => {}
+            }
         });
         Ok(None)
     }
 
+    pub(crate) fn shutdown(&self) {
+        self.shutdown_token.cancel();
+    }
+
     async fn apps_list_task(
         outgoing: Arc<OutgoingMessageSender>,
         request_id: ConnectionRequestId,
diff --git a/codex-rs/app-server/src/skills_watcher.rs b/codex-rs/app-server/src/skills_watcher.rs
index d20628d3866d..9e34cdac8e3d 100644
--- a/codex-rs/app-server/src/skills_watcher.rs
+++ b/codex-rs/app-server/src/skills_watcher.rs
@@ -15,6 +15,8 @@ use codex_file_watcher::ThrottledWatchReceiver;
 use codex_file_watcher::WatchPath;
 use codex_file_watcher::WatchRegistration;
 use codex_protocol::protocol::TurnEnvironmentSelection;
+use tokio_util::sync::CancellationToken;
+use tokio_util::sync::DropGuard;
 use tracing::warn;
 
 #[cfg(not(test))]
@@ -24,6 +26,8 @@ const WATCHER_THROTTLE_INTERVAL: Duration = Duration::from_millis(50);
 
 pub(crate) struct SkillsWatcher {
     subscriber: FileWatcherSubscriber,
+    shutdown_token: CancellationToken,
+    _shutdown_drop_guard: DropGuard,
 }
 
 impl SkillsWatcher {
@@ -39,8 +43,18 @@ impl SkillsWatcher {
             }
         };
         let (subscriber, rx) = file_watcher.add_subscriber();
-        Self::spawn_event_loop(rx, skills_manager, outgoing);
-        Arc::new(Self { subscriber })
+        let shutdown_token = CancellationToken::new();
+        let shutdown_drop_guard = shutdown_token.clone().drop_guard();
+        Self::spawn_event_loop(rx, skills_manager, outgoing, shutdown_token.child_token());
+        Arc::new(Self {
+            subscriber,
+            shutdown_token,
+            _shutdown_drop_guard: shutdown_drop_guard,
+        })
+    }
+
+    pub(crate) fn shutdown(&self) {
+        self.shutdown_token.cancel();
     }
 
     pub(crate) async fn register_thread_config(
@@ -92,6 +106,7 @@ impl SkillsWatcher {
         rx: Receiver,
         skills_manager: Arc<SkillsManager>,
         outgoing: Arc<OutgoingMessageSender>,
+        shutdown_token: CancellationToken,
     ) {
         let mut rx = ThrottledWatchReceiver::new(rx, WATCHER_THROTTLE_INTERVAL);
         let Ok(handle) = tokio::runtime::Handle::try_current() else {
@@ -99,7 +114,14 @@ impl SkillsWatcher {
             return;
         };
         handle.spawn(async move {
-            while rx.recv().await.is_some() {
+            loop {
+                let event = tokio::select! {
+                    _ = shutdown_token.cancelled() => break,
+                    event = rx.recv() => event,
+                };
+                if event.is_none() {
+                    break;
+                }
                 skills_manager.clear_cache();
                 outgoing
                     .send_server_notification(ServerNotification::SkillsChanged(