diff --git a/src/automations/commander.ts b/src/automations/commander.ts
index b520d00..709a4ce 100644
--- a/src/automations/commander.ts
+++ b/src/automations/commander.ts
@@ -39,7 +39,7 @@ export default class Commander {
   static initCommand = async (): Promise<void> => {
 
     // hide active windows
-    window.hideActiveWindows();
+    await window.hideWindows();
     await window.releaseFocus();
 
     // grab text
diff --git a/src/main.ts b/src/main.ts
index 8e5d70b..acd1b39 100644
--- a/src/main.ts
+++ b/src/main.ts
@@ -319,10 +319,10 @@ ipcMain.on('run-command', async (event, payload) => {
   commander = null;
   
   // cancelled
+  window.restoreWindows();
   if (result.cancelled) return;
 
   // show chat window
-  window.restoreWindows();
   if (result?.chatWindow) {
     await wait();
     result.chatWindow.show();
@@ -337,11 +337,16 @@ ipcMain.on('run-command', async (event, payload) => {
 
 ipcMain.on('stop-command', async () => {
 
+  // cancel any running command
   if (commander !== null) {
-    commander.cancelCommand();
+    await commander.cancelCommand();
     commander = null;
   }
 
+  // restore windows
+  await window.restoreWindows();
+  await window.releaseFocus();
+
 });
 
 ipcMain.on('run-python-code', async (event, payload) => {
diff --git a/src/main/window.ts b/src/main/window.ts
index d38c10a..67fa660 100644
--- a/src/main/window.ts
+++ b/src/main/window.ts
@@ -181,15 +181,15 @@ export const openChatWindow = (params: strDict) => {
 };
 
 let windowsToRestore: BrowserWindow[] = [];
-export const hideActiveWindows = async () => {
+export const hideWindows = async () => {
 
   // remember to restore all windows
   windowsToRestore = [];
   try {
-    console.log('Hiding active windows');
+    console.log('Hiding windows');
     const windows = BrowserWindow.getAllWindows();
     for (const window of windows) {
-      if (!window.isDestroyed() && window.isVisible() && !window.isFocused() && !window.isMinimized()) {
+      if (!window.isDestroyed() && window.isVisible() && !window.isMinimized()) {
         windowsToRestore.push(window);
         window.hide();
       }
@@ -203,19 +203,25 @@ export const hideActiveWindows = async () => {
 
 export const restoreWindows = () => {
   if (windowsToRestore.length) {
-    console.log('Restoring active windows')
-    if (windowsToRestore.includes(mainWindow)) {
-      mainWindow.showInactive();
-    }
+    console.log(`Restoring ${windowsToRestore.length} windows`)
+
+    // restore main window first
+    windowsToRestore.sort((a, b) => {
+      if (a === mainWindow) return -1;
+      if (b === mainWindow) return 1;
+      return 0;
+    })
+
+    // now restore
     for (const window of windowsToRestore) {
       try {
-        if (window != mainWindow) {
-          window.showInactive();
-        }
+        window.showInactive();
       } catch (error) {
         console.error('Error while restoring window', error);
       }
     }
+
+    // done
     windowsToRestore = [];
   }
 };
diff --git a/tests/unit/commander.test.ts b/tests/unit/commander.test.ts
index 23bd0e5..e25b0b5 100644
--- a/tests/unit/commander.test.ts
+++ b/tests/unit/commander.test.ts
@@ -24,7 +24,7 @@ vi.mock('../../src/main/window.ts', async () => {
     openWaitingPanel: vi.fn(),
     closeWaitingPanel: vi.fn(),
     openChatWindow: vi.fn(),
-    hideActiveWindows: vi.fn(),
+    hideWindows: vi.fn(),
     releaseFocus: vi.fn()
   }
 })
@@ -82,7 +82,7 @@ test('Prepare command', async () => {
 
   await Commander.initCommand()
 
-  expect(window.hideActiveWindows).toHaveBeenCalledOnce()
+  expect(window.hideWindows).toHaveBeenCalledOnce()
   expect(window.releaseFocus).toHaveBeenCalledOnce()
   expect(Automator.prototype.getSelectedText).toHaveBeenCalledOnce()
   expect(window.openCommandPalette).toHaveBeenCalledOnce()