diff --git a/Source/Core/Core/Core.cpp b/Source/Core/Core/Core.cpp
index 760d16d95d..128a2a228d 100644
--- a/Source/Core/Core/Core.cpp
+++ b/Source/Core/Core/Core.cpp
@@ -481,6 +481,16 @@ static void EmuThread(std::unique_ptr<BootParameters> boot)
     INFO_LOG(CONSOLE, "%s", StopMessage(false, "Shutting down HW").c_str());
     HW::Shutdown();
     INFO_LOG(CONSOLE, "%s", StopMessage(false, "HW shutdown").c_str());
+
+    // Clear on screen messages that haven't expired
+    OSD::ClearMessages();
+
+    // The config must be restored only after the whole HW has shut down,
+    // not when it is still running.
+    BootManager::RestoreConfig();
+
+    PatchEngine::Shutdown();
+    HLE::Clear();
   }};
 
   if (!g_video_backend->Initialize(s_window_handle))
@@ -638,13 +648,6 @@ static void EmuThread(std::unique_ptr<BootParameters> boot)
   if (core_parameter.bCPUThread)
     g_video_backend->Video_Cleanup();
 
-  // Clear on screen messages that haven't expired
-  OSD::ClearMessages();
-
-  BootManager::RestoreConfig();
-
-  PatchEngine::Shutdown();
-  HLE::Clear();
   // If we shut down normally, the stop message does not need to be triggered.
   stop_message_guard.Dismiss();
 }