diff --git a/Source/Core/Core/BootManager.cpp b/Source/Core/Core/BootManager.cpp
index 52a3ec910f..5dcf2a3f5a 100644
--- a/Source/Core/Core/BootManager.cpp
+++ b/Source/Core/Core/BootManager.cpp
@@ -32,7 +32,6 @@
 #include "Core/AchievementManager.h"
 #include "Core/Boot/Boot.h"
 #include "Core/Config/MainSettings.h"
-#include "Core/Config/SYSCONFSettings.h"
 #include "Core/ConfigLoaders/BaseConfigLoader.h"
 #include "Core/ConfigLoaders/NetPlayConfigLoader.h"
 #include "Core/ConfigManager.h"
@@ -148,6 +147,8 @@ bool BootCore(Core::System& system, std::unique_ptr<BootParameters> boot,
 
   Core::UpdateWantDeterminism(system, /*initial*/ true);
 
+  ConfigLoaders::TransferSYSCONFControlToGuest();
+
   if (system.IsWii())
   {
     Core::InitializeWiiRoot(Core::WantsDeterminism());
@@ -156,13 +157,16 @@ bool BootCore(Core::System& system, std::unique_ptr<BootParameters> boot,
     if (!Core::WantsDeterminism())
     {
       Core::BackupWiiSettings();
-      ConfigLoaders::SaveToSYSCONF(Config::LayerType::Meta);
+      ConfigLoaders::SaveToSYSCONF(Config::LayerType::Meta,
+                                   ConfigLoaders::SkipIfControlledByGuest::No);
     }
     else
     {
-      ConfigLoaders::SaveToSYSCONF(Config::LayerType::Meta, [](const Config::Location& location) {
-        return Config::GetActiveLayerForConfig(location) >= Config::LayerType::Movie;
-      });
+      ConfigLoaders::SaveToSYSCONF(
+          Config::LayerType::Meta, ConfigLoaders::SkipIfControlledByGuest::No,
+          [](const Config::Location& location) {
+            return Config::GetActiveLayerForConfig(location) >= Config::LayerType::Movie;
+          });
     }
   }
 
@@ -183,35 +187,6 @@ bool BootCore(Core::System& system, std::unique_ptr<BootParameters> boot,
   return Core::Init(system, std::move(boot), wsi);
 }
 
-// SYSCONF can be modified during emulation by the user and internally, which makes it
-// a bad idea to just always overwrite it with the settings from the base layer.
-//
-// Conversely, we also shouldn't just accept any changes to SYSCONF, as it may cause
-// temporary settings (from Movie, Netplay, game INIs, etc.) to stick around.
-//
-// To avoid inconveniences in most cases, we accept changes that aren't being overriden by a
-// non-base layer, and restore only the overriden settings.
-static void RestoreSYSCONF()
-{
-  // This layer contains the new SYSCONF settings (including any temporary settings).
-  Config::Layer temp_layer(Config::LayerType::Base);
-  // Use a separate loader so the temp layer doesn't automatically save
-  ConfigLoaders::GenerateBaseConfigLoader()->Load(&temp_layer);
-
-  for (const auto& setting : Config::SYSCONF_SETTINGS)
-  {
-    std::visit(
-        [&](auto* info) {
-          // If this setting was overridden, then we copy the base layer value back to the SYSCONF.
-          // Otherwise we leave the new value in the SYSCONF.
-          if (Config::GetActiveLayerForConfig(*info) == Config::LayerType::Base)
-            Config::SetBase(*info, temp_layer.Get(*info));
-        },
-        setting.config_info);
-  }
-  ConfigLoaders::SaveToSYSCONF(Config::LayerType::Base);
-}
-
 void RestoreConfig()
 {
   Core::ShutdownWiiRoot();
@@ -219,7 +194,11 @@ void RestoreConfig()
   if (!Core::WiiRootIsTemporary())
   {
     Core::RestoreWiiSettings(Core::RestoreReason::EmulationEnd);
-    RestoreSYSCONF();
+    ConfigLoaders::TransferSYSCONFControlFromGuest(ConfigLoaders::WriteBackChangedValues::Yes);
+  }
+  else
+  {
+    ConfigLoaders::TransferSYSCONFControlFromGuest(ConfigLoaders::WriteBackChangedValues::No);
   }
 
   Config::ClearCurrentRunLayer();
diff --git a/Source/Core/Core/ConfigLoaders/BaseConfigLoader.cpp b/Source/Core/Core/ConfigLoaders/BaseConfigLoader.cpp
index 88fa7c0696..959428aec2 100644
--- a/Source/Core/Core/ConfigLoaders/BaseConfigLoader.cpp
+++ b/Source/Core/Core/ConfigLoaders/BaseConfigLoader.cpp
@@ -9,12 +9,14 @@
 #include <list>
 #include <map>
 #include <memory>
+#include <mutex>
 #include <string>
 #include <type_traits>
 #include <variant>
 
 #include "Common/CommonTypes.h"
 #include "Common/Config/Config.h"
+#include "Common/Config/Layer.h"
 #include "Common/FileUtil.h"
 #include "Common/IniFile.h"
 #include "Common/Logging/Log.h"
@@ -23,17 +25,67 @@
 #include "Core/Config/SYSCONFSettings.h"
 #include "Core/ConfigLoaders/IsSettingSaveable.h"
 #include "Core/ConfigManager.h"
-#include "Core/Core.h"
 #include "Core/IOS/IOS.h"
 #include "Core/IOS/USB/Bluetooth/BTBase.h"
 #include "Core/SysConf.h"
 #include "Core/System.h"
 
+static bool s_sysconf_controlled_by_guest = false;
+static std::recursive_mutex s_sysconf_lock;
+
 namespace ConfigLoaders
 {
-void SaveToSYSCONF(Config::LayerType layer, std::function<bool(const Config::Location&)> predicate)
+void TransferSYSCONFControlToGuest()
 {
-  if (Core::IsRunning(Core::System::GetInstance()))
+  std::lock_guard lock(s_sysconf_lock);
+
+  ASSERT(!s_sysconf_controlled_by_guest);
+  s_sysconf_controlled_by_guest = true;
+}
+
+void TransferSYSCONFControlFromGuest(WriteBackChangedValues write_back_changed_values)
+{
+  std::lock_guard lock(s_sysconf_lock);
+
+  ASSERT(s_sysconf_controlled_by_guest);
+  s_sysconf_controlled_by_guest = false;
+
+  if (write_back_changed_values == WriteBackChangedValues::Yes)
+  {
+    // SYSCONF can be modified during emulation by the user and internally, which makes it
+    // a bad idea to just always overwrite it with the settings from the base layer.
+    //
+    // Conversely, we also shouldn't just accept any changes to SYSCONF, as it may cause
+    // temporary settings (from Movie, Netplay, game INIs, etc.) to stick around.
+    //
+    // To avoid inconveniences in most cases, we accept changes that aren't being overriden by a
+    // non-base layer, and restore only the overriden settings.
+
+    // This layer contains the new SYSCONF settings (including any temporary settings).
+    Config::Layer temp_layer(Config::LayerType::Base);
+    // Use a separate loader so the temp layer doesn't automatically save
+    GenerateBaseConfigLoader()->Load(&temp_layer);
+
+    for (const auto& setting : Config::SYSCONF_SETTINGS)
+    {
+      std::visit(
+          [&](auto* info) {
+            // If this setting was overridden, then we copy the base layer value back to the
+            // SYSCONF. Otherwise we leave the new value in the SYSCONF.
+            if (Config::GetActiveLayerForConfig(*info) == Config::LayerType::Base)
+              Config::SetBase(*info, temp_layer.Get(*info));
+          },
+          setting.config_info);
+    }
+    ConfigLoaders::SaveToSYSCONF(Config::LayerType::Base);
+  }
+}
+
+void SaveToSYSCONF(Config::LayerType layer, SkipIfControlledByGuest skip,
+                   std::function<bool(const Config::Location&)> predicate)
+{
+  std::lock_guard lock(s_sysconf_lock);
+  if (skip != SkipIfControlledByGuest::No && s_sysconf_controlled_by_guest)
     return;
 
   IOS::HLE::Kernel ios;
@@ -183,7 +235,8 @@ public:
 private:
   void LoadFromSYSCONF(Config::Layer* layer)
   {
-    if (Core::IsRunning(Core::System::GetInstance()))
+    std::lock_guard lock(s_sysconf_lock);
+    if (s_sysconf_controlled_by_guest)
       return;
 
     IOS::HLE::Kernel ios;
diff --git a/Source/Core/Core/ConfigLoaders/BaseConfigLoader.h b/Source/Core/Core/ConfigLoaders/BaseConfigLoader.h
index 7c20a5e065..e07fc690e4 100644
--- a/Source/Core/Core/ConfigLoaders/BaseConfigLoader.h
+++ b/Source/Core/Core/ConfigLoaders/BaseConfigLoader.h
@@ -15,7 +15,22 @@ struct Location;
 
 namespace ConfigLoaders
 {
+enum class WriteBackChangedValues
+{
+  No,
+  Yes,
+};
+
+enum class SkipIfControlledByGuest
+{
+  No,
+  Yes,
+};
+
+void TransferSYSCONFControlToGuest();
+void TransferSYSCONFControlFromGuest(WriteBackChangedValues write_back_changed_values);
 void SaveToSYSCONF(Config::LayerType layer,
+                   SkipIfControlledByGuest skip = SkipIfControlledByGuest::Yes,
                    std::function<bool(const Config::Location&)> predicate = {});
 std::unique_ptr<Config::ConfigLayerLoader> GenerateBaseConfigLoader();
 }  // namespace ConfigLoaders