diff --git a/.changeset/pretty-parts-admire.md b/.changeset/pretty-parts-admire.md
new file mode 100644
index 0000000000..87c27295d5
--- /dev/null
+++ b/.changeset/pretty-parts-admire.md
@@ -0,0 +1,5 @@
+---
+'@backstage/core-components': patch
+---
+
+Fix autologout not working correctly when closing all tabs
diff --git a/packages/core-components/src/components/AutoLogout/AutoLogout.tsx b/packages/core-components/src/components/AutoLogout/AutoLogout.tsx
index 932ac7432b..4f53ce4bd7 100644
--- a/packages/core-components/src/components/AutoLogout/AutoLogout.tsx
+++ b/packages/core-components/src/components/AutoLogout/AutoLogout.tsx
@@ -114,6 +114,7 @@ const ConditionalAutoLogout = ({
     // Events will be rebound as long as `stopOnMount` is not set.
     setPromptOpen(false);
     setRemainingTimeCountdown(0);
+    lastSeenOnlineStore.delete();
     identityApi.signOut();
   };
 
@@ -231,18 +232,37 @@ const parseConfig = (
 export const AutoLogout = (props: AutoLogoutProps): JSX.Element | null => {
   const identityApi = useApi(identityApiRef);
   const configApi = useApi(configApiRef);
-  const [isLogged, setIsLogged] = useState(false);
+  const [isLogged, setIsLogged] = useState<boolean | null>(null);
+  const lastSeenOnlineStore: TimestampStore = useMemo(
+    () => new DefaultTimestampStore(LAST_SEEN_ONLINE_STORAGE_KEY),
+    [],
+  );
+
   useEffect(() => {
-    // if the user is not logged in, the autologout feature won't affect the app even if enabled
-    async function isLoggedIn(identity: IdentityApi) {
-      if ((await identity.getCredentials()).token) {
-        setIsLogged(true);
-      } else {
+    let cancelled = false;
+
+    async function checkLogin(identity: IdentityApi) {
+      try {
+        const creds = await identity.getCredentials();
+        if (cancelled) return;
+        if (creds?.token) {
+          setIsLogged(true);
+        } else {
+          setIsLogged(false);
+          lastSeenOnlineStore.delete();
+        }
+      } catch (err) {
+        if (cancelled) return;
         setIsLogged(false);
+        lastSeenOnlineStore.delete();
       }
     }
-    isLoggedIn(identityApi);
-  }, [identityApi]);
+    checkLogin(identityApi);
+
+    return () => {
+      cancelled = true;
+    };
+  }, [lastSeenOnlineStore, identityApi]);
 
   const {
     enabled,
@@ -274,10 +294,6 @@ export const AutoLogout = (props: AutoLogoutProps): JSX.Element | null => {
     }
   }, [idleTimeoutMinutes, promptBeforeIdleSeconds]);
 
-  const lastSeenOnlineStore: TimestampStore = useMemo(
-    () => new DefaultTimestampStore(LAST_SEEN_ONLINE_STORAGE_KEY),
-    [],
-  );
   const [promptOpen, setPromptOpen] = useState<boolean>(false);
 
   const [remainingTimeCountdown, setRemainingTimeCountdown] =
@@ -285,7 +301,8 @@ export const AutoLogout = (props: AutoLogoutProps): JSX.Element | null => {
 
   useLogoutDisconnectedUserEffect({
     enableEffect: logoutIfDisconnected,
-    autologoutIsEnabled: enabled && isLogged,
+    autologoutIsEnabled: enabled,
+    isLoggedIn: isLogged,
     idleTimeoutSeconds: idleTimeoutMinutes * 60,
     lastSeenOnlineStore,
     identityApi,
diff --git a/packages/core-components/src/components/AutoLogout/disconnectedUsers.test.ts b/packages/core-components/src/components/AutoLogout/disconnectedUsers.test.ts
index 3d097dcc7f..e6fbbc7161 100644
--- a/packages/core-components/src/components/AutoLogout/disconnectedUsers.test.ts
+++ b/packages/core-components/src/components/AutoLogout/disconnectedUsers.test.ts
@@ -35,10 +35,29 @@ const mockTimestampStore = {
 };
 
 describe('useLogoutDisconnectedUserEffect', () => {
-  it('should not do anything if effect is not enabled', () => {
+  it('should not do anything if isLoggedIn has not yet resolved', () => {
+    const props: UseLogoutDisconnectedUserEffectProps = {
+      enableEffect: true,
+      autologoutIsEnabled: true,
+      isLoggedIn: null,
+      idleTimeoutSeconds: 300,
+      lastSeenOnlineStore: mockTimestampStore,
+      identityApi: mockIdentityApi,
+    };
+
+    renderHook(() => useLogoutDisconnectedUserEffect(props));
+
+    expect(mockTimestampStore.get).not.toHaveBeenCalled();
+    expect(mockTimestampStore.delete).not.toHaveBeenCalled();
+    expect(mockTimestampStore.save).not.toHaveBeenCalled();
+    expect(mockIdentityApi.signOut).not.toHaveBeenCalled();
+  });
+
+  it('should not do anything if effect is not enabled and isLoggedIn is false', () => {
     const props: UseLogoutDisconnectedUserEffectProps = {
       enableEffect: false,
       autologoutIsEnabled: true,
+      isLoggedIn: false,
       idleTimeoutSeconds: 300,
       lastSeenOnlineStore: mockTimestampStore,
       identityApi: mockIdentityApi,
@@ -54,6 +73,7 @@ describe('useLogoutDisconnectedUserEffect', () => {
     const props: UseLogoutDisconnectedUserEffectProps = {
       enableEffect: true,
       autologoutIsEnabled: false,
+      isLoggedIn: true,
       idleTimeoutSeconds: 300,
       lastSeenOnlineStore: mockTimestampStore,
       identityApi: mockIdentityApi,
@@ -64,12 +84,34 @@ describe('useLogoutDisconnectedUserEffect', () => {
     expect(mockTimestampStore.delete).toHaveBeenCalled();
   });
 
+  it('should delete the store and sign out when idle timeout has passed', () => {
+    const staleStore = {
+      ...mockTimestampStore,
+      get: jest.fn().mockReturnValue(new Date(Date.now() - 2000)),
+    };
+    const props: UseLogoutDisconnectedUserEffectProps = {
+      enableEffect: true,
+      autologoutIsEnabled: true,
+      isLoggedIn: true,
+      idleTimeoutSeconds: 1,
+      lastSeenOnlineStore: staleStore,
+      identityApi: mockIdentityApi,
+    };
+
+    renderHook(() => useLogoutDisconnectedUserEffect(props));
+
+    expect(staleStore.delete).toHaveBeenCalled();
+    expect(mockIdentityApi.signOut).toHaveBeenCalled();
+    expect(staleStore.save).not.toHaveBeenCalled();
+  });
+
   it('should call signOut if idle timeout passed', () => {
     jest.useFakeTimers();
 
     const props: UseLogoutDisconnectedUserEffectProps = {
       enableEffect: true,
       autologoutIsEnabled: true,
+      isLoggedIn: true,
       idleTimeoutSeconds: 1,
       lastSeenOnlineStore: {
         ...mockTimestampStore,
@@ -93,6 +135,7 @@ describe('useLogoutDisconnectedUserEffect', () => {
     const props: UseLogoutDisconnectedUserEffectProps = {
       enableEffect: true,
       autologoutIsEnabled: true,
+      isLoggedIn: true,
       idleTimeoutSeconds: 300,
       lastSeenOnlineStore: mockTimestampStore,
       identityApi: mockIdentityApi,
diff --git a/packages/core-components/src/components/AutoLogout/disconnectedUsers.ts b/packages/core-components/src/components/AutoLogout/disconnectedUsers.ts
index c09e272eaa..4d1d8bf833 100644
--- a/packages/core-components/src/components/AutoLogout/disconnectedUsers.ts
+++ b/packages/core-components/src/components/AutoLogout/disconnectedUsers.ts
@@ -24,6 +24,7 @@ export const LAST_SEEN_ONLINE_STORAGE_KEY =
 export type UseLogoutDisconnectedUserEffectProps = {
   enableEffect: boolean;
   autologoutIsEnabled: boolean;
+  isLoggedIn: boolean | null;
   idleTimeoutSeconds: number;
   lastSeenOnlineStore: TimestampStore;
   identityApi: IdentityApi;
@@ -32,6 +33,7 @@ export type UseLogoutDisconnectedUserEffectProps = {
 export const useLogoutDisconnectedUserEffect = ({
   enableEffect,
   autologoutIsEnabled,
+  isLoggedIn,
   idleTimeoutSeconds,
   lastSeenOnlineStore,
   identityApi,
@@ -41,30 +43,34 @@ export const useLogoutDisconnectedUserEffect = ({
      * Considers disconnected users as inactive users.
      * If all Backstage tabs are closed and idleTimeoutMinutes are passed then logout the user anyway.
      */
-    if (autologoutIsEnabled && enableEffect) {
-      const lastSeenOnline = lastSeenOnlineStore.get();
-      if (lastSeenOnline) {
-        const now = new Date();
-        const nowSeconds = Math.ceil(now.getTime() / 1000);
-        const lastSeenOnlineSeconds = Math.ceil(
-          lastSeenOnline.getTime() / 1000,
-        );
-        if (nowSeconds - lastSeenOnlineSeconds > idleTimeoutSeconds) {
-          identityApi.signOut();
-        }
-      }
-      /**
-       * save for the first time when app is loaded, so that
-       * if user logs in and does nothing we still have a
-       * lastSeenOnline value in store
-       */
-      lastSeenOnlineStore.save(new Date());
-    } else {
-      lastSeenOnlineStore.delete();
+    const shouldCheckDisconnectedUser = autologoutIsEnabled && enableEffect;
+
+    // Prevent lastSeen getting deleted before logged state is checked
+    if (isLoggedIn === null) {
+      return;
     }
+
+    if (!shouldCheckDisconnectedUser || !isLoggedIn) {
+      lastSeenOnlineStore.delete();
+      return;
+    }
+
+    const lastSeenOnline = lastSeenOnlineStore.get();
+    if (lastSeenOnline) {
+      const now = new Date();
+      const nowSeconds = Math.ceil(now.getTime() / 1000);
+      const lastSeenOnlineSeconds = Math.ceil(lastSeenOnline.getTime() / 1000);
+      if (nowSeconds - lastSeenOnlineSeconds > idleTimeoutSeconds) {
+        lastSeenOnlineStore.delete();
+        identityApi.signOut();
+        return;
+      }
+    }
+    lastSeenOnlineStore.save(new Date());
   }, [
     autologoutIsEnabled,
     enableEffect,
+    isLoggedIn,
     identityApi,
     idleTimeoutSeconds,
     lastSeenOnlineStore,