diff --git a/quickstep/src/com/android/launcher3/taskbar/ManageWindowsTaskbarShortcut.kt b/quickstep/src/com/android/launcher3/taskbar/ManageWindowsTaskbarShortcut.kt
index 032eb5151e..75ce7c3dd5 100644
--- a/quickstep/src/com/android/launcher3/taskbar/ManageWindowsTaskbarShortcut.kt
+++ b/quickstep/src/com/android/launcher3/taskbar/ManageWindowsTaskbarShortcut.kt
@@ -148,11 +148,19 @@ class ManageWindowsTaskbarShortcut<T>(
                         FLAG_AUTOHIDE_SUSPEND_MULTI_INSTANCE_MENU_OPEN,
                         false,
                     )
+                    controllers.taskbarPopupController.cleanUpMultiInstanceMenuReference()
                 }
             }
         )
     }
 
+    /** Closes the multi-instance menu if it has been initialized. */
+    fun closeMultiInstanceMenu() {
+        if (::taskbarShortcutAllWindowsView.isInitialized) {
+            taskbarShortcutAllWindowsView.animateClose()
+        }
+    }
+
     /**
      * A view container for displaying the window of open instances of an app
      *
@@ -238,6 +246,7 @@ class ManageWindowsTaskbarShortcut<T>(
             )
             taskbarOverlayContext.dragLayer?.removeView(menuView.rootView)
             taskbarOverlayContext.dragLayer.removeTouchController(this)
+            controllers.taskbarPopupController.cleanUpMultiInstanceMenuReference()
         }
 
         /** TouchController implementations for closing the carousel when touched outside */
diff --git a/quickstep/src/com/android/launcher3/taskbar/TaskbarActivityContext.java b/quickstep/src/com/android/launcher3/taskbar/TaskbarActivityContext.java
index 8e2246bfdb..54270955b2 100644
--- a/quickstep/src/com/android/launcher3/taskbar/TaskbarActivityContext.java
+++ b/quickstep/src/com/android/launcher3/taskbar/TaskbarActivityContext.java
@@ -1422,6 +1422,7 @@ public class TaskbarActivityContext extends BaseTaskbarContext {
             Log.e(TAG, "Unknown type clicked: " + tag);
         }
 
+        mControllers.taskbarPopupController.maybeCloseMultiInstanceMenu();
         if (shouldCloseAllOpenViews) {
             AbstractFloatingView.closeAllOpenViews(this);
         }
diff --git a/quickstep/src/com/android/launcher3/taskbar/TaskbarPopupController.java b/quickstep/src/com/android/launcher3/taskbar/TaskbarPopupController.java
index abf35a21b9..afd317bbb5 100644
--- a/quickstep/src/com/android/launcher3/taskbar/TaskbarPopupController.java
+++ b/quickstep/src/com/android/launcher3/taskbar/TaskbarPopupController.java
@@ -86,6 +86,8 @@ public class TaskbarPopupController implements TaskbarControllers.LoggableTaskba
     private TaskbarControllers mControllers;
     private boolean mAllowInitialSplitSelection;
     private AppInfo[] mAppInfosList;
+    private ManageWindowsTaskbarShortcut<BaseTaskbarContext> mManageWindowsTaskbarShortcut;
+
 
     public TaskbarPopupController(TaskbarActivityContext context) {
         mContext = context;
@@ -111,6 +113,19 @@ public class TaskbarPopupController implements TaskbarControllers.LoggableTaskba
         mPopupDataProvider.setDeepShortcutMap(deepShortcutMapCopy);
     }
 
+    /** Closes the multi-instance menu if it is enabled and currently open. */
+    public void maybeCloseMultiInstanceMenu() {
+        if (Flags.enableMultiInstanceMenuTaskbar() && mManageWindowsTaskbarShortcut != null) {
+            mManageWindowsTaskbarShortcut.closeMultiInstanceMenu();
+            cleanUpMultiInstanceMenuReference();
+        }
+    }
+
+    /** Releases the reference to the Taskbar multi-instance menu */
+    public void cleanUpMultiInstanceMenuReference() {
+        mManageWindowsTaskbarShortcut = null;
+    }
+
     public void setAllowInitialSplitSelection(boolean allowInitialSplitSelection) {
         mAllowInitialSplitSelection = allowInitialSplitSelection;
     }
@@ -206,6 +221,7 @@ public class TaskbarPopupController implements TaskbarControllers.LoggableTaskba
         if (Flags.enableMultiInstanceMenuTaskbar()
                 && DesktopModeStatus.canEnterDesktopMode(mContext)
                 && !mControllers.taskbarStashController.isInOverview()) {
+            maybeCloseMultiInstanceMenu();
             shortcuts.addAll(getMultiInstanceMenuOptions().toList());
         }
         return shortcuts.stream();
@@ -325,8 +341,9 @@ public class TaskbarPopupController implements TaskbarControllers.LoggableTaskba
     public SystemShortcut.Factory<BaseTaskbarContext> createManageWindowsShortcutFactory() {
         return (context, itemInfo, originalView) -> {
             if (shouldShowMultiInstanceOptions(itemInfo)) {
-                return new ManageWindowsTaskbarShortcut<>(context, itemInfo, originalView,
-                        mControllers);
+                mManageWindowsTaskbarShortcut = new ManageWindowsTaskbarShortcut<>(
+                        context, itemInfo, originalView, mControllers);
+                return mManageWindowsTaskbarShortcut;
             }
             return null;
         };
diff --git a/quickstep/src/com/android/launcher3/taskbar/allapps/TaskbarAllAppsController.java b/quickstep/src/com/android/launcher3/taskbar/allapps/TaskbarAllAppsController.java
index 07d86e4e78..ddbf3b7fc6 100644
--- a/quickstep/src/com/android/launcher3/taskbar/allapps/TaskbarAllAppsController.java
+++ b/quickstep/src/com/android/launcher3/taskbar/allapps/TaskbarAllAppsController.java
@@ -141,6 +141,7 @@ public final class TaskbarAllAppsController {
         if (isOpen()) {
             mSlideInView.close(true);
         } else {
+            mControllers.taskbarPopupController.maybeCloseMultiInstanceMenu();
             show(true, showKeyboard);
         }
     }