diff --git a/src/NDS.cpp b/src/NDS.cpp
index 3ebaf442..cd762d7e 100644
--- a/src/NDS.cpp
+++ b/src/NDS.cpp
@@ -346,6 +346,7 @@ void Reset()
 void Stop()
 {
     printf("Stopping: shutdown\n");
+    Running = false;
     Platform::StopEmu();
     GPU::Stop();
     SPU::Stop();
diff --git a/src/libui_sdl/Platform.cpp b/src/libui_sdl/Platform.cpp
index cebc74d5..0b1e0a2d 100644
--- a/src/libui_sdl/Platform.cpp
+++ b/src/libui_sdl/Platform.cpp
@@ -44,7 +44,7 @@
 #endif
 
 
-void Stop();
+void Stop(bool internal);
 
 
 namespace Platform
@@ -75,7 +75,7 @@ u8 PacketBuffer[2048];
 
 void StopEmu()
 {
-    Stop();
+    Stop(true);
 }
 
 
diff --git a/src/libui_sdl/main.cpp b/src/libui_sdl/main.cpp
index f27c7eda..241d9b76 100644
--- a/src/libui_sdl/main.cpp
+++ b/src/libui_sdl/main.cpp
@@ -320,10 +320,11 @@ void Run()
     uiMenuItemSetChecked(MenuItem_Pause, 0);
 }
 
-void Stop()
+void Stop(bool internal)
 {
     EmuRunning = 2;
-    while (EmuStatus != 2);
+    if (!internal) // if shutting down from the UI thread, wait till the emu thread has stopped
+        while (EmuStatus != 2);
     RunningSomething = false;
 
     uiMenuItemDisable(MenuItem_Pause);
@@ -449,7 +450,7 @@ void OnStop(uiMenuItem* item, uiWindow* window, void* blarg)
 {
     if (!RunningSomething) return;
 
-    Stop();
+    Stop(false);
 }
 
 void OnOpenEmuSettings(uiMenuItem* item, uiWindow* window, void* blarg)