diff --git a/Source/Android/jni/Config/NativeConfig.cpp b/Source/Android/jni/Config/NativeConfig.cpp
index 8478174dae..c524c0ea9e 100644
--- a/Source/Android/jni/Config/NativeConfig.cpp
+++ b/Source/Android/jni/Config/NativeConfig.cpp
@@ -11,7 +11,6 @@
 #include "Core/ConfigLoaders/GameConfigLoader.h"
 #include "Core/ConfigLoaders/IsSettingSaveable.h"
 #include "jni/AndroidCommon/AndroidCommon.h"
-#include "jni/Host.h"
 
 constexpr jint LAYER_BASE_OR_CURRENT = 0;
 constexpr jint LAYER_BASE = 1;
@@ -143,10 +142,6 @@ Java_org_dolphinemu_dolphinemu_features_settings_model_NativeConfig_unloadGameIn
 JNIEXPORT void JNICALL Java_org_dolphinemu_dolphinemu_features_settings_model_NativeConfig_save(
     JNIEnv*, jclass, jint layer)
 {
-  // HostThreadLock is used to ensure we don't try to save to SYSCONF at the same time as
-  // emulation shutdown does
-  HostThreadLock guard;
-
   return GetLayer(layer, {})->Save();
 }
 
diff --git a/Source/Core/Core/BootManager.cpp b/Source/Core/Core/BootManager.cpp
index ae49a14b92..c5a526d262 100644
--- a/Source/Core/Core/BootManager.cpp
+++ b/Source/Core/Core/BootManager.cpp
@@ -26,7 +26,6 @@
 #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"
@@ -138,6 +137,8 @@ bool BootCore(Core::System& system, std::unique_ptr<BootParameters> boot,
 
   Core::UpdateWantDeterminism(system, /*initial*/ true);
 
+  ConfigLoaders::TransferSYSCONFControlToGuest();
+
   if (system.IsWii())
   {
     Core::InitializeWiiRoot(Core::WantsDeterminism());
@@ -146,13 +147,16 @@ 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;
+          });
     }
   }
 
@@ -173,43 +177,18 @@ 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 overridden by a
-// non-base layer, and restore only the overridden 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();
 
-  if (!Core::WiiRootIsTemporary())
+  if (Core::WiiRootIsTemporary())
+  {
+    ConfigLoaders::TransferSYSCONFControlFromGuest(ConfigLoaders::WriteBackChangedValues::No);
+  }
+  else
   {
     Core::RestoreWiiSettings(Core::RestoreReason::EmulationEnd);
-    RestoreSYSCONF();
+    ConfigLoaders::TransferSYSCONFControlFromGuest(ConfigLoaders::WriteBackChangedValues::Yes);
   }
 
   Config::ClearCurrentRunLayer();
diff --git a/Source/Core/Core/ConfigLoaders/BaseConfigLoader.cpp b/Source/Core/Core/ConfigLoaders/BaseConfigLoader.cpp
index 811eb9974e..8b35d4d684 100644
--- a/Source/Core/Core/ConfigLoaders/BaseConfigLoader.cpp
+++ b/Source/Core/Core/ConfigLoaders/BaseConfigLoader.cpp
@@ -8,11 +8,13 @@
 #include <functional>
 #include <map>
 #include <memory>
+#include <mutex>
 #include <string>
 #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"
@@ -21,17 +23,68 @@
 #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::No)
+    return;
+
+  // 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 overridden by a
+  // non-base layer, and restore only the overridden 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);
+  }
+
+  SaveToSYSCONF(Config::LayerType::Base, SkipIfControlledByGuest::No);
+}
+
+void SaveToSYSCONF(Config::LayerType layer, SkipIfControlledByGuest skip,
+                   std::function<bool(const Config::Location&)> predicate)
+{
+  std::lock_guard lock(s_sysconf_lock);
+  if (skip == SkipIfControlledByGuest::Yes && s_sysconf_controlled_by_guest)
     return;
 
   IOS::HLE::Kernel ios;
@@ -125,7 +178,7 @@ public:
 
   void Save(Config::Layer* layer) override
   {
-    SaveToSYSCONF(layer->GetLayer());
+    SaveToSYSCONF(layer->GetLayer(), SkipIfControlledByGuest::Yes);
 
     std::map<Config::System, Common::IniFile> inis;
 
@@ -180,7 +233,8 @@ 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..30a6d26e4b 100644
--- a/Source/Core/Core/ConfigLoaders/BaseConfigLoader.h
+++ b/Source/Core/Core/ConfigLoaders/BaseConfigLoader.h
@@ -15,7 +15,21 @@ struct Location;
 
 namespace ConfigLoaders
 {
-void SaveToSYSCONF(Config::LayerType layer,
+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,
                    std::function<bool(const Config::Location&)> predicate = {});
 std::unique_ptr<Config::ConfigLayerLoader> GenerateBaseConfigLoader();
 }  // namespace ConfigLoaders