diff --git a/Source/Core/Core/Core.cpp b/Source/Core/Core/Core.cpp
index 760d16d95d..75b36ef0fd 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();
 }
@@ -961,7 +964,10 @@ void UpdateWantDeterminism(bool initial)
     // We need to clear the cache because some parts of the JIT depend on want_determinism, e.g. use
     // of FMA.
     JitInterface::ClearCache();
-    Core::InitializeWiiRoot(s_wants_determinism);
+
+    // Don't call InitializeWiiRoot during boot, because IOS already does it.
+    if (!initial)
+      Core::InitializeWiiRoot(s_wants_determinism);
 
     Core::PauseAndLock(false, was_unpaused);
   }
diff --git a/Source/Core/Core/WiiRoot.cpp b/Source/Core/Core/WiiRoot.cpp
index 995e633522..7a2f5104b3 100644
--- a/Source/Core/Core/WiiRoot.cpp
+++ b/Source/Core/Core/WiiRoot.cpp
@@ -16,10 +16,6 @@
 #include "Core/Movie.h"
 #include "Core/NetPlayClient.h"
 
-#ifdef _WIN32
-#include <Windows.h>
-#endif
-
 namespace Core
 {
 static std::string s_temp_wii_root;
@@ -56,8 +52,6 @@ static void InitializeDeterministicWiiSaves()
 
 void InitializeWiiRoot(bool use_temporary)
 {
-  ShutdownWiiRoot();
-
   if (use_temporary)
   {
     s_temp_wii_root = File::CreateTempDir();
@@ -69,12 +63,6 @@ void InitializeWiiRoot(bool use_temporary)
     File::CopyDir(File::GetSysDirectory() + WII_USER_DIR, s_temp_wii_root);
     WARN_LOG(IOS_FILEIO, "Using temporary directory %s for minimal Wii FS",
              s_temp_wii_root.c_str());
-    static bool s_registered;
-    if (!s_registered)
-    {
-      s_registered = true;
-      atexit(ShutdownWiiRoot);
-    }
     File::SetUserPath(D_SESSION_WIIROOT_IDX, s_temp_wii_root);
     // Generate a SYSCONF with default settings for the temporary Wii NAND.
     SysConf sysconf{Common::FromWhichRoot::FROM_SESSION_ROOT};