diff --git a/src/frontend/qt_sdl/EmuInstance.cpp b/src/frontend/qt_sdl/EmuInstance.cpp
index f4092b61..89d4108b 100644
--- a/src/frontend/qt_sdl/EmuInstance.cpp
+++ b/src/frontend/qt_sdl/EmuInstance.cpp
@@ -154,8 +154,6 @@ EmuInstance::~EmuInstance()
     deleting = true;
     deleteAllWindows();
 
-    MPInterface::Get().End(instanceID);
-
     emuThread->emuExit();
     emuThread->wait();
     delete emuThread;
diff --git a/src/frontend/qt_sdl/EmuThread.cpp b/src/frontend/qt_sdl/EmuThread.cpp
index 6417fa69..f767c6db 100644
--- a/src/frontend/qt_sdl/EmuThread.cpp
+++ b/src/frontend/qt_sdl/EmuThread.cpp
@@ -478,7 +478,8 @@ void EmuThread::waitMessage(int num)
 void EmuThread::waitAllMessages()
 {
     if (QThread::currentThread() == this) return;
-    msgSemaphore.acquire(msgSemaphore.available());
+    while (!msgQueue.empty())
+        msgSemaphore.acquire();
 }
 
 void EmuThread::handleMessages()
@@ -494,6 +495,7 @@ void EmuThread::handleMessages()
             emuPauseStack = emuPauseStackRunning;
 
             emuInstance->audioDisable();
+            MPInterface::Get().End(emuInstance->instanceID);
             break;
 
         case msg_EmuRun: