diff --git a/Source/Core/Core/Core.cpp b/Source/Core/Core/Core.cpp
index 604de6f170..c37a5df922 100644
--- a/Source/Core/Core/Core.cpp
+++ b/Source/Core/Core/Core.cpp
@@ -277,8 +277,6 @@ void Stop()  // - Hammertime!
 
 		g_video_backend->Video_ExitLoop();
 	}
-	if (s_emu_thread.joinable())
-		s_emu_thread.join();
 }
 
 static void DeclareAsCPUThread()
@@ -813,6 +811,18 @@ 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 1eea2be226..9fd256c388 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 c89e0d8307..19a53332f4 100644
--- a/Source/Core/DolphinWX/Main.cpp
+++ b/Source/Core/DolphinWX/Main.cpp
@@ -364,6 +364,7 @@ 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 1389abdcee..604e75216a 100644
--- a/Source/Core/DolphinWX/MainAndroid.cpp
+++ b/Source/Core/DolphinWX/MainAndroid.cpp
@@ -622,6 +622,7 @@ 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 9186742d46..60c7c7a0ee 100644
--- a/Source/Core/DolphinWX/MainNoGUI.cpp
+++ b/Source/Core/DolphinWX/MainNoGUI.cpp
@@ -359,6 +359,7 @@ int main(int argc, char* argv[])
 	while (PowerPC::GetState() != PowerPC::CPU_POWERDOWN)
 		updateMainFrameEvent.Wait();
 
+	Core::Shutdown();
 	platform->Shutdown();
 	UICommon::Shutdown();