diff --git a/Windows/EmuThread.cpp b/Windows/EmuThread.cpp
index 27a34fcc7b..03a8124725 100644
--- a/Windows/EmuThread.cpp
+++ b/Windows/EmuThread.cpp
@@ -59,6 +59,7 @@ void MainThread_Start(bool separateEmuThread) {
 void MainThread_Stop() {
 	// Already stopped?
 	UpdateUIState(UISTATE_EXIT);
+	Core_Stop();
 	mainThread.join();
 }