diff --git a/Windows/EmuThread.cpp b/Windows/EmuThread.cpp
index 4ce78cfdcd..c18450c007 100644
--- a/Windows/EmuThread.cpp
+++ b/Windows/EmuThread.cpp
@@ -298,7 +298,6 @@ void MainThreadFunc() {
 		Core_StateProcessed();
 		NativeFrame(graphicsContext);
 	}
-	Core_WaitInactive();
 
 	g_inLoop = false;
 
diff --git a/Windows/MainWindow.cpp b/Windows/MainWindow.cpp
index b448a1de85..10a1778099 100644
--- a/Windows/MainWindow.cpp
+++ b/Windows/MainWindow.cpp
@@ -929,9 +929,9 @@ namespace MainWindow
 		case WM_DESTROY:
 			g_InputManager.StopPolling();
 			g_InputManager.Shutdown();
+			WindowsRawInput::Shutdown();
 
 			MainThread_Stop();
-			WindowsRawInput::Shutdown();
 			KillTimer(hWnd, TIMER_CURSORUPDATE);
 			KillTimer(hWnd, TIMER_CURSORMOVEUPDATE);
 			// Main window is gone, this tells the message loop to exit.