diff --git a/Source/Core/Core/Core.cpp b/Source/Core/Core/Core.cpp
index 84ced6b876..7db5e458ce 100644
--- a/Source/Core/Core/Core.cpp
+++ b/Source/Core/Core/Core.cpp
@@ -162,7 +162,7 @@ void DisplayMessage(const std::string& message, int time_in_ms)
 
 bool IsRunning()
 {
-	return (GetState() != CORE_UNINITIALIZED) || s_hardware_initialized;
+	return (GetState() != CORE_UNINITIALIZED || s_hardware_initialized) && !s_is_stopping;
 }
 
 bool IsRunningAndStarted()
@@ -273,8 +273,6 @@ void Stop()  // - Hammertime!
 
 		g_video_backend->Video_ExitLoop();
 	}
-	if (s_emu_thread.joinable())
-		s_emu_thread.join();
 }
 
 static void DeclareAsCPUThread()
@@ -829,6 +827,18 @@ void UpdateTitle()
 	Host_UpdateTitle(SMessage);
 }
 
+void Shutdown()
+{
+	// During shutdown DXGI expects us to handle some messages on the UI thread.
+	// Therefore we can't immediately block and wait for the emu thread to shut
+	// down, so we join the emu thread as late as possible when the UI has already
+	// shut down.
+	// For more info read "DirectX Graphics Infrastructure (DXGI): Best Practices"
+	// on MSDN.
+	if (s_emu_thread.joinable())
+		s_emu_thread.join();
+}
+
 void SetOnStoppedCallback(StoppedCallbackFunc callback)
 {
 	s_on_stopped_callback = callback;
diff --git a/Source/Core/Core/Core.h b/Source/Core/Core/Core.h
index 11d4fa2e98..0bafa5e2d9 100644
--- a/Source/Core/Core/Core.h
+++ b/Source/Core/Core/Core.h
@@ -39,6 +39,7 @@ enum EState
 
 bool Init();
 void Stop();
+void Shutdown();
 
 std::string StopMessage(bool, const std::string&);
 
diff --git a/Source/Core/DolphinWX/Main.cpp b/Source/Core/DolphinWX/Main.cpp
index 194ca7b566..43a79ac6f7 100644
--- a/Source/Core/DolphinWX/Main.cpp
+++ b/Source/Core/DolphinWX/Main.cpp
@@ -370,6 +370,7 @@ void DolphinApp::OnEndSession(wxCloseEvent& event)
 
 int DolphinApp::OnExit()
 {
+	Core::Shutdown();
 	UICommon::Shutdown();
 
 	delete m_locale;
diff --git a/Source/Core/DolphinWX/MainAndroid.cpp b/Source/Core/DolphinWX/MainAndroid.cpp
index 3788f42928..1d48f5c103 100644
--- a/Source/Core/DolphinWX/MainAndroid.cpp
+++ b/Source/Core/DolphinWX/MainAndroid.cpp
@@ -627,6 +627,7 @@ JNIEXPORT void JNICALL Java_org_dolphinemu_dolphinemu_NativeLibrary_Run(JNIEnv *
 			updateMainFrameEvent.Wait();
 	}
 
+	Core::Shutdown();
 	UICommon::Shutdown();
 	ANativeWindow_release(surf);
 
diff --git a/Source/Core/DolphinWX/MainNoGUI.cpp b/Source/Core/DolphinWX/MainNoGUI.cpp
index 1f559b9f88..5d50423f0a 100644
--- a/Source/Core/DolphinWX/MainNoGUI.cpp
+++ b/Source/Core/DolphinWX/MainNoGUI.cpp
@@ -358,6 +358,7 @@ int main(int argc, char* argv[])
 	while (PowerPC::GetState() != PowerPC::CPU_POWERDOWN)
 		updateMainFrameEvent.Wait();
 
+	Core::Shutdown();
 	platform->Shutdown();
 	UICommon::Shutdown();