diff --git a/src/citra_qt/bootmanager.cpp b/src/citra_qt/bootmanager.cpp
index d9bacfc3d..9aec16506 100644
--- a/src/citra_qt/bootmanager.cpp
+++ b/src/citra_qt/bootmanager.cpp
@@ -72,6 +72,9 @@ void EmuThread::run() {
         }
     }
 
+    // Shutdown the core emulation
+    System::Shutdown();
+
     MicroProfileOnThreadExit();
 
     render_window->moveContext();
diff --git a/src/citra_qt/main.cpp b/src/citra_qt/main.cpp
index 7fb1b0dcb..11813a2a8 100644
--- a/src/citra_qt/main.cpp
+++ b/src/citra_qt/main.cpp
@@ -283,9 +283,6 @@ void GMainWindow::ShutdownGame() {
     emu_thread->wait();
     emu_thread = nullptr;
 
-    // Shutdown the core emulation
-    System::Shutdown();
-
     // Update the GUI
     ui.action_Start->setEnabled(false);
     ui.action_Start->setText(tr("Start"));