diff --git a/Source/Core/Core/BootManager.cpp b/Source/Core/Core/BootManager.cpp
index a5e0f434c1..1a16b7e95a 100644
--- a/Source/Core/Core/BootManager.cpp
+++ b/Source/Core/Core/BootManager.cpp
@@ -44,6 +44,7 @@
 #include "Core/Movie.h"
 #include "Core/NetPlayProto.h"
 #include "Core/PowerPC/PowerPC.h"
+#include "Core/System.h"
 #include "Core/WiiRoot.h"
 
 #include "DiscIO/Enums.h"
@@ -69,12 +70,6 @@ public:
 
 private:
   bool valid = false;
-  bool bCPUThread = false;
-  bool bMMU = false;
-  bool bSyncGPU = false;
-  int iSyncGpuMaxDistance = 0;
-  int iSyncGpuMinDistance = 0;
-  float fSyncGpuOverclock = 0;
   std::array<WiimoteSource, MAX_BBMOTES> iWiimoteSource{};
 };
 
@@ -82,13 +77,6 @@ void ConfigCache::SaveConfig(const SConfig& config)
 {
   valid = true;
 
-  bCPUThread = config.bCPUThread;
-  bMMU = config.bMMU;
-  bSyncGPU = config.bSyncGPU;
-  iSyncGpuMaxDistance = config.iSyncGpuMaxDistance;
-  iSyncGpuMinDistance = config.iSyncGpuMinDistance;
-  fSyncGpuOverclock = config.fSyncGpuOverclock;
-
   for (int i = 0; i != MAX_BBMOTES; ++i)
     iWiimoteSource[i] = WiimoteCommon::GetSource(i);
 
@@ -103,13 +91,6 @@ void ConfigCache::RestoreConfig(SConfig* config)
 
   valid = false;
 
-  config->bCPUThread = bCPUThread;
-  config->bMMU = bMMU;
-  config->bSyncGPU = bSyncGPU;
-  config->iSyncGpuMaxDistance = iSyncGpuMaxDistance;
-  config->iSyncGpuMinDistance = iSyncGpuMinDistance;
-  config->fSyncGpuOverclock = fSyncGpuOverclock;
-
   // Only change these back if they were actually set by game ini, since they can be changed while a
   // game is running.
   if (config->bWii)
@@ -143,13 +124,8 @@ bool BootCore(std::unique_ptr<BootParameters> boot, const WindowSystemInfo& wsi)
     IniFile game_ini = StartUp.LoadGameIni();
 
     // General settings
-    IniFile::Section* core_section = game_ini.GetOrCreateSection("Core");
     IniFile::Section* controls_section = game_ini.GetOrCreateSection("Controls");
 
-    core_section->Get("CPUThread", &StartUp.bCPUThread, StartUp.bCPUThread);
-    core_section->Get("MMU", &StartUp.bMMU, StartUp.bMMU);
-    core_section->Get("SyncGPU", &StartUp.bSyncGPU, StartUp.bSyncGPU);
-
     // Wii settings
     if (StartUp.bWii)
     {
@@ -180,9 +156,6 @@ bool BootCore(std::unique_ptr<BootParameters> boot, const WindowSystemInfo& wsi)
   // Movie settings
   if (Movie::IsPlayingInput() && Movie::IsConfigSaved())
   {
-    // TODO: remove this once ConfigManager starts using OnionConfig.
-    StartUp.bCPUThread = Config::Get(Config::MAIN_CPU_THREAD);
-    StartUp.bSyncGPU = Config::Get(Config::MAIN_SYNC_GPU);
     for (int i = 0; i < 2; ++i)
     {
       if (Movie::IsUsingMemcard(i) && Movie::IsStartingFromClearSave() && !StartUp.bWii)
@@ -203,13 +176,7 @@ bool BootCore(std::unique_ptr<BootParameters> boot, const WindowSystemInfo& wsi)
   {
     const NetPlay::NetSettings& netplay_settings = NetPlay::GetNetSettings();
     Config::AddLayer(ConfigLoaders::GenerateNetPlayConfigLoader(netplay_settings));
-    StartUp.bCPUThread = netplay_settings.m_CPUthread;
     StartUp.bCopyWiiSaveNetplay = netplay_settings.m_CopyWiiSave;
-    StartUp.bSyncGPU = netplay_settings.m_SyncGPU;
-    StartUp.iSyncGpuMaxDistance = netplay_settings.m_SyncGpuMaxDistance;
-    StartUp.iSyncGpuMinDistance = netplay_settings.m_SyncGpuMinDistance;
-    StartUp.fSyncGpuOverclock = netplay_settings.m_SyncGpuOverclock;
-    StartUp.bMMU = netplay_settings.m_MMU;
   }
   else
   {
@@ -263,6 +230,8 @@ bool BootCore(std::unique_ptr<BootParameters> boot, const WindowSystemInfo& wsi)
   if (!boot->riivolution_patches.empty())
     Config::SetCurrent(Config::MAIN_FAST_DISC_SPEED, true);
 
+  Core::System::GetInstance().Initialize();
+
   Core::UpdateWantDeterminism(/*initial*/ true);
 
   if (StartUp.bWii)
diff --git a/Source/Core/Core/ConfigLoaders/IsSettingSaveable.cpp b/Source/Core/Core/ConfigLoaders/IsSettingSaveable.cpp
index a505a815ae..575582a205 100644
--- a/Source/Core/Core/ConfigLoaders/IsSettingSaveable.cpp
+++ b/Source/Core/Core/ConfigLoaders/IsSettingSaveable.cpp
@@ -117,6 +117,13 @@ bool IsSettingSaveable(const Config::Location& config_location)
       &Config::GetInfoForSIDevice(1).GetLocation(),
       &Config::GetInfoForSIDevice(2).GetLocation(),
       &Config::GetInfoForSIDevice(3).GetLocation(),
+      &Config::MAIN_CPU_THREAD.GetLocation(),
+      &Config::MAIN_MMU.GetLocation(),
+      &Config::MAIN_BB_DUMP_PORT.GetLocation(),
+      &Config::MAIN_SYNC_GPU.GetLocation(),
+      &Config::MAIN_SYNC_GPU_MAX_DISTANCE.GetLocation(),
+      &Config::MAIN_SYNC_GPU_MIN_DISTANCE.GetLocation(),
+      &Config::MAIN_SYNC_GPU_OVERCLOCK.GetLocation(),
 
       // UI.General
 
diff --git a/Source/Core/Core/ConfigManager.cpp b/Source/Core/Core/ConfigManager.cpp
index bd2942e487..2d90207601 100644
--- a/Source/Core/Core/ConfigManager.cpp
+++ b/Source/Core/Core/ConfigManager.cpp
@@ -84,50 +84,13 @@ SConfig::~SConfig()
 void SConfig::SaveSettings()
 {
   NOTICE_LOG_FMT(BOOT, "Saving settings to {}", File::GetUserPath(F_DOLPHINCONFIG_IDX));
-  IniFile ini;
-  ini.Load(File::GetUserPath(F_DOLPHINCONFIG_IDX));  // load first to not kill unknown stuff
-
-  SaveCoreSettings(ini);
-
-  ini.Save(File::GetUserPath(F_DOLPHINCONFIG_IDX));
-
   Config::Save();
 }
 
-void SConfig::SaveCoreSettings(IniFile& ini)
-{
-  IniFile::Section* core = ini.GetOrCreateSection("Core");
-
-  core->Set("CPUThread", bCPUThread);
-  core->Set("SyncGPU", bSyncGPU);
-  core->Set("SyncGpuMaxDistance", iSyncGpuMaxDistance);
-  core->Set("SyncGpuMinDistance", iSyncGpuMinDistance);
-  core->Set("SyncGpuOverclock", fSyncGpuOverclock);
-  core->Set("MMU", bMMU);
-}
-
 void SConfig::LoadSettings()
 {
-  Config::Load();
-
   INFO_LOG_FMT(BOOT, "Loading Settings from {}", File::GetUserPath(F_DOLPHINCONFIG_IDX));
-  IniFile ini;
-  ini.Load(File::GetUserPath(F_DOLPHINCONFIG_IDX));
-
-  LoadCoreSettings(ini);
-}
-
-void SConfig::LoadCoreSettings(IniFile& ini)
-{
-  IniFile::Section* core = ini.GetOrCreateSection("Core");
-
-  core->Get("CPUThread", &bCPUThread, true);
-  core->Get("MMU", &bMMU, bMMU);
-  core->Get("BBDumpPort", &iBBDumpPort, -1);
-  core->Get("SyncGPU", &bSyncGPU, false);
-  core->Get("SyncGpuMaxDistance", &iSyncGpuMaxDistance, 200000);
-  core->Get("SyncGpuMinDistance", &iSyncGpuMinDistance, -200000);
-  core->Get("SyncGpuOverclock", &fSyncGpuOverclock, 1.0f);
+  Config::Load();
 }
 
 void SConfig::ResetRunningGameMetadata()
@@ -243,10 +206,6 @@ void SConfig::LoadDefaults()
   bAutomaticStart = false;
   bBootToPause = false;
 
-  bCPUThread = false;
-  bMMU = false;
-  iBBDumpPort = -1;
-  bSyncGPU = false;
   bWii = false;
 
   ResetRunningGameMetadata();
diff --git a/Source/Core/Core/ConfigManager.h b/Source/Core/Core/ConfigManager.h
index a8a1c70fdf..9125eabcb3 100644
--- a/Source/Core/Core/ConfigManager.h
+++ b/Source/Core/Core/ConfigManager.h
@@ -56,17 +56,8 @@ struct SConfig
   bool bJITNoBlockCache = false;
   bool bJITNoBlockLinking = false;
 
-  bool bCPUThread = true;
   bool bCopyWiiSaveNetplay = true;
 
-  bool bMMU = false;
-  int iBBDumpPort = 0;
-
-  bool bSyncGPU = false;
-  int iSyncGpuMaxDistance;
-  int iSyncGpuMinDistance;
-  float fSyncGpuOverclock;
-
   bool bWii = false;
   bool m_is_mios = false;
 
@@ -134,10 +125,6 @@ private:
   SConfig();
   ~SConfig();
 
-  void SaveCoreSettings(IniFile& ini);
-
-  void LoadCoreSettings(IniFile& ini);
-
   void SetRunningGameMetadata(const std::string& game_id, const std::string& gametdb_id,
                               u64 title_id, u16 revision, DiscIO::Region region);
 
diff --git a/Source/Core/Core/Core.cpp b/Source/Core/Core/Core.cpp
index df575b431f..1687c9900f 100644
--- a/Source/Core/Core/Core.cpp
+++ b/Source/Core/Core/Core.cpp
@@ -67,6 +67,7 @@
 #include "Core/PowerPC/JitInterface.h"
 #include "Core/PowerPC/PowerPC.h"
 #include "Core/State.h"
+#include "Core/System.h"
 #include "Core/WiiRoot.h"
 
 #ifdef USE_MEMORYWATCHER
@@ -202,8 +203,7 @@ bool IsCPUThread()
 
 bool IsGPUThread()
 {
-  const SConfig& _CoreParameter = SConfig::GetInstance();
-  if (_CoreParameter.bCPUThread)
+  if (Core::System::GetInstance().IsDualCoreMode())
   {
     return (s_emu_thread.joinable() && (s_emu_thread.get_id() == std::this_thread::get_id()));
   }
@@ -238,7 +238,8 @@ bool Init(std::unique_ptr<BootParameters> boot, const WindowSystemInfo& wsi)
   HostDispatchJobs();
 
   INFO_LOG_FMT(BOOT, "Starting core = {} mode", SConfig::GetInstance().bWii ? "Wii" : "GameCube");
-  INFO_LOG_FMT(BOOT, "CPU Thread separate = {}", SConfig::GetInstance().bCPUThread ? "Yes" : "No");
+  INFO_LOG_FMT(BOOT, "CPU Thread separate = {}",
+               Core::System::GetInstance().IsDualCoreMode() ? "Yes" : "No");
 
   Host_UpdateMainFrame();  // Disable any menus or buttons at boot
 
@@ -272,8 +273,6 @@ void Stop()  // - Hammertime!
   if (GetState() == State::Stopping || GetState() == State::Uninitialized)
     return;
 
-  const SConfig& _CoreParameter = SConfig::GetInstance();
-
   s_is_stopping = true;
 
   s_timer.Stop();
@@ -291,7 +290,7 @@ void Stop()  // - Hammertime!
   INFO_LOG_FMT(CONSOLE, "{}", StopMessage(true, "Stop CPU"));
   CPU::Stop();
 
-  if (_CoreParameter.bCPUThread)
+  if (Core::System::GetInstance().IsDualCoreMode())
   {
     // Video_EnterLoop() should now exit so that EmuThread()
     // will continue concurrently with the rest of the commands
@@ -333,8 +332,7 @@ static void CpuThread(const std::optional<std::string>& savestate_path, bool del
 {
   DeclareAsCPUThread();
 
-  const SConfig& _CoreParameter = SConfig::GetInstance();
-  if (_CoreParameter.bCPUThread)
+  if (Core::System::GetInstance().IsDualCoreMode())
     Common::SetCurrentThreadName("CPU thread");
   else
     Common::SetCurrentThreadName("CPU-GPU thread");
@@ -413,8 +411,7 @@ static void FifoPlayerThread(const std::optional<std::string>& savestate_path,
 {
   DeclareAsCPUThread();
 
-  const SConfig& _CoreParameter = SConfig::GetInstance();
-  if (_CoreParameter.bCPUThread)
+  if (Core::System::GetInstance().IsDualCoreMode())
     Common::SetCurrentThreadName("FIFO player thread");
   else
     Common::SetCurrentThreadName("FIFO-GPU thread");
@@ -446,6 +443,7 @@ static void FifoPlayerThread(const std::optional<std::string>& savestate_path,
 // See the BootManager.cpp file description for a complete call schedule.
 static void EmuThread(std::unique_ptr<BootParameters> boot, WindowSystemInfo wsi)
 {
+  const Core::System& system = Core::System::GetInstance();
   const SConfig& core_parameter = SConfig::GetInstance();
   CallOnStateChangedCallbacks(State::Starting);
   Common::ScopeGuard flag_guard{[] {
@@ -647,7 +645,7 @@ static void EmuThread(std::unique_ptr<BootParameters> boot, WindowSystemInfo wsi
   }
 
   // ENTER THE VIDEO THREAD LOOP
-  if (core_parameter.bCPUThread)
+  if (system.IsDualCoreMode())
   {
     // This thread, after creating the EmuWindow, spawns a CPU
     // thread, and then takes over and becomes the video thread
@@ -930,8 +928,6 @@ void Callback_NewField()
 
 void UpdateTitle(u32 ElapseTime)
 {
-  SConfig& _CoreParameter = SConfig::GetInstance();
-
   if (ElapseTime == 0)
     ElapseTime = 1;
 
@@ -942,8 +938,9 @@ void UpdateTitle(u32 ElapseTime)
 
   // Settings are shown the same for both extended and summary info
   const std::string SSettings = fmt::format(
-      "{} {} | {} | {}", PowerPC::GetCPUName(), _CoreParameter.bCPUThread ? "DC" : "SC",
-      g_video_backend->GetDisplayName(), Config::Get(Config::MAIN_DSP_HLE) ? "HLE" : "LLE");
+      "{} {} | {} | {}", PowerPC::GetCPUName(),
+      Core::System::GetInstance().IsDualCoreMode() ? "DC" : "SC", g_video_backend->GetDisplayName(),
+      Config::Get(Config::MAIN_DSP_HLE) ? "HLE" : "LLE");
 
   std::string SFPS;
   if (Movie::IsPlayingInput())
diff --git a/Source/Core/Core/DolphinAnalytics.cpp b/Source/Core/Core/DolphinAnalytics.cpp
index 93ed3888dd..d03ee0f0f3 100644
--- a/Source/Core/Core/DolphinAnalytics.cpp
+++ b/Source/Core/Core/DolphinAnalytics.cpp
@@ -359,9 +359,9 @@ void DolphinAnalytics::MakePerGameBuilder()
   builder.AddData("cfg-dsp-hle", Config::Get(Config::MAIN_DSP_HLE));
   builder.AddData("cfg-dsp-jit", Config::Get(Config::MAIN_DSP_JIT));
   builder.AddData("cfg-dsp-thread", Config::Get(Config::MAIN_DSP_THREAD));
-  builder.AddData("cfg-cpu-thread", SConfig::GetInstance().bCPUThread);
+  builder.AddData("cfg-cpu-thread", Config::Get(Config::MAIN_CPU_THREAD));
   builder.AddData("cfg-fastmem", Config::Get(Config::MAIN_FASTMEM));
-  builder.AddData("cfg-syncgpu", SConfig::GetInstance().bSyncGPU);
+  builder.AddData("cfg-syncgpu", Config::Get(Config::MAIN_SYNC_GPU));
   builder.AddData("cfg-audio-backend", Config::Get(Config::MAIN_AUDIO_BACKEND));
   builder.AddData("cfg-oc-enable", Config::Get(Config::MAIN_OVERCLOCK_ENABLE));
   builder.AddData("cfg-oc-factor", Config::Get(Config::MAIN_OVERCLOCK));
diff --git a/Source/Core/Core/HW/Memmap.cpp b/Source/Core/Core/HW/Memmap.cpp
index a9c942660b..ed0fc3a2d4 100644
--- a/Source/Core/Core/HW/Memmap.cpp
+++ b/Source/Core/Core/HW/Memmap.cpp
@@ -33,6 +33,7 @@
 #include "Core/HW/WII_IPC.h"
 #include "Core/PowerPC/JitCommon/JitBase.h"
 #include "Core/PowerPC/PowerPC.h"
+#include "Core/System.h"
 #include "VideoCommon/CommandProcessor.h"
 #include "VideoCommon/PixelEngine.h"
 
@@ -260,7 +261,7 @@ void Init()
                            false};
 
   const bool wii = SConfig::GetInstance().bWii;
-  const bool mmu = SConfig::GetInstance().bMMU;
+  const bool mmu = Core::System::GetInstance().IsMMUMode();
 
   bool fake_vmem = false;
 #ifndef _ARCH_32
diff --git a/Source/Core/Core/HW/WiimoteReal/WiimoteReal.cpp b/Source/Core/Core/HW/WiimoteReal/WiimoteReal.cpp
index 1c57dff7ef..4f2896ad49 100644
--- a/Source/Core/Core/HW/WiimoteReal/WiimoteReal.cpp
+++ b/Source/Core/Core/HW/WiimoteReal/WiimoteReal.cpp
@@ -303,11 +303,11 @@ void Wiimote::Read()
 
   if (result > 0)
   {
-    if (SConfig::GetInstance().iBBDumpPort > 0 && m_index == WIIMOTE_BALANCE_BOARD)
+    if (m_balance_board_dump_port > 0 && m_index == WIIMOTE_BALANCE_BOARD)
     {
       static sf::UdpSocket Socket;
       Socket.send((char*)rpt.data(), rpt.size(), sf::IpAddress::LocalHost,
-                  SConfig::GetInstance().iBBDumpPort);
+                  m_balance_board_dump_port);
     }
 
     // Add it to queue
@@ -324,11 +324,10 @@ bool Wiimote::Write()
 
   Report const& rpt = m_write_reports.Front();
 
-  if (SConfig::GetInstance().iBBDumpPort > 0 && m_index == WIIMOTE_BALANCE_BOARD)
+  if (m_balance_board_dump_port > 0 && m_index == WIIMOTE_BALANCE_BOARD)
   {
     static sf::UdpSocket Socket;
-    Socket.send((char*)rpt.data(), rpt.size(), sf::IpAddress::LocalHost,
-                SConfig::GetInstance().iBBDumpPort);
+    Socket.send((char*)rpt.data(), rpt.size(), sf::IpAddress::LocalHost, m_balance_board_dump_port);
   }
   int ret = IOWrite(rpt.data(), rpt.size());
 
@@ -816,6 +815,7 @@ void Wiimote::ThreadFunc()
 void Wiimote::RefreshConfig()
 {
   m_speaker_enabled_in_dolphin_config = Config::Get(Config::MAIN_WIIMOTE_ENABLE_SPEAKER);
+  m_balance_board_dump_port = Config::Get(Config::MAIN_BB_DUMP_PORT);
 }
 
 int Wiimote::GetIndex() const
diff --git a/Source/Core/Core/HW/WiimoteReal/WiimoteReal.h b/Source/Core/Core/HW/WiimoteReal/WiimoteReal.h
index 34573a0609..487d28024f 100644
--- a/Source/Core/Core/HW/WiimoteReal/WiimoteReal.h
+++ b/Source/Core/Core/HW/WiimoteReal/WiimoteReal.h
@@ -148,6 +148,7 @@ private:
   Common::SPSCQueue<Report> m_write_reports;
 
   bool m_speaker_enabled_in_dolphin_config = false;
+  int m_balance_board_dump_port = 0;
 
   size_t m_config_changed_callback_id;
 };
diff --git a/Source/Core/Core/PowerPC/JitArm64/Jit.cpp b/Source/Core/Core/PowerPC/JitArm64/Jit.cpp
index 28c229d6c6..bdcf40fdfc 100644
--- a/Source/Core/Core/PowerPC/JitArm64/Jit.cpp
+++ b/Source/Core/Core/PowerPC/JitArm64/Jit.cpp
@@ -48,7 +48,7 @@ JitArm64::~JitArm64() = default;
 
 void JitArm64::Init()
 {
-  const size_t child_code_size = SConfig::GetInstance().bMMU ? FARCODE_SIZE_MMU : FARCODE_SIZE;
+  const size_t child_code_size = m_mmu_enabled ? FARCODE_SIZE_MMU : FARCODE_SIZE;
   AllocCodeSpace(CODE_SIZE + child_code_size);
   AddChildCodeSpace(&m_far_code, child_code_size);
 
diff --git a/Source/Core/Core/PowerPC/JitCommon/JitBase.cpp b/Source/Core/Core/PowerPC/JitCommon/JitBase.cpp
index 5dfe40cfd4..392aca5f0d 100644
--- a/Source/Core/Core/PowerPC/JitCommon/JitBase.cpp
+++ b/Source/Core/Core/PowerPC/JitCommon/JitBase.cpp
@@ -10,6 +10,7 @@
 #include "Core/HW/CPU.h"
 #include "Core/PowerPC/PPCAnalyst.h"
 #include "Core/PowerPC/PowerPC.h"
+#include "Core/System.h"
 
 const u8* JitBase::Dispatch(JitBase& jit)
 {
@@ -55,6 +56,7 @@ void JitBase::RefreshConfig()
   m_fprf = Config::Get(Config::MAIN_FPRF);
   m_accurate_nans = Config::Get(Config::MAIN_ACCURATE_NANS);
   m_fastmem_enabled = Config::Get(Config::MAIN_FASTMEM);
+  m_mmu_enabled = Core::System::GetInstance().IsMMUMode();
   analyzer.SetDebuggingEnabled(m_enable_debugging);
   analyzer.SetBranchFollowingEnabled(Config::Get(Config::MAIN_JIT_FOLLOW_BRANCH));
   analyzer.SetFloatExceptionsEnabled(m_enable_float_exceptions);
@@ -80,7 +82,7 @@ void JitBase::UpdateMemoryAndExceptionOptions()
 {
   bool any_watchpoints = PowerPC::memchecks.HasAny();
   jo.fastmem = m_fastmem_enabled && jo.fastmem_arena && (MSR.DR || !any_watchpoints);
-  jo.memcheck = SConfig::GetInstance().bMMU || any_watchpoints;
+  jo.memcheck = m_mmu_enabled || any_watchpoints;
   jo.fp_exceptions = m_enable_float_exceptions;
   jo.div_by_zero_exceptions = m_enable_div_by_zero_exceptions;
 }
diff --git a/Source/Core/Core/PowerPC/JitCommon/JitBase.h b/Source/Core/Core/PowerPC/JitCommon/JitBase.h
index d9e7ae8e94..9cd47722e7 100644
--- a/Source/Core/Core/PowerPC/JitCommon/JitBase.h
+++ b/Source/Core/Core/PowerPC/JitCommon/JitBase.h
@@ -133,6 +133,7 @@ protected:
   bool m_fprf = false;
   bool m_accurate_nans = false;
   bool m_fastmem_enabled = false;
+  bool m_mmu_enabled = false;
 
   void RefreshConfig();
 
diff --git a/Source/Core/Core/PowerPC/MMU.cpp b/Source/Core/Core/PowerPC/MMU.cpp
index 54d2ac21f8..869a7a8648 100644
--- a/Source/Core/Core/PowerPC/MMU.cpp
+++ b/Source/Core/Core/PowerPC/MMU.cpp
@@ -21,6 +21,7 @@
 #include "Core/PowerPC/GDBStub.h"
 #include "Core/PowerPC/JitInterface.h"
 #include "Core/PowerPC/PowerPC.h"
+#include "Core/System.h"
 
 #include "VideoCommon/VideoBackendBase.h"
 
@@ -1147,7 +1148,7 @@ TranslateResult JitCache_TranslateAddress(u32 address)
 static void GenerateDSIException(u32 effective_address, bool write)
 {
   // DSI exceptions are only supported in MMU mode.
-  if (!SConfig::GetInstance().bMMU)
+  if (!Core::System::GetInstance().IsMMUMode())
   {
     PanicAlertFmt("Invalid {} {:#010x}, PC = {:#010x}", write ? "write to" : "read from",
                   effective_address, PC);
diff --git a/Source/Core/Core/System.cpp b/Source/Core/Core/System.cpp
index f13d28d6b1..e7e14ea91e 100644
--- a/Source/Core/Core/System.cpp
+++ b/Source/Core/Core/System.cpp
@@ -3,6 +3,8 @@
 
 #include "Core/System.h"
 
+#include "Core/Config/MainSettings.h"
+
 namespace Core
 {
 struct System::Impl
@@ -14,4 +16,10 @@ System::System() : m_impl{std::make_unique<Impl>()}
 }
 
 System::~System() = default;
+
+void System::Initialize()
+{
+  m_separate_cpu_and_gpu_threads = Config::Get(Config::MAIN_CPU_THREAD);
+  m_mmu_enabled = Config::Get(Config::MAIN_MMU);
+}
 }  // namespace Core
diff --git a/Source/Core/Core/System.h b/Source/Core/Core/System.h
index 23a29aa0ca..14d48ce477 100644
--- a/Source/Core/Core/System.h
+++ b/Source/Core/Core/System.h
@@ -26,10 +26,18 @@ public:
     return instance;
   }
 
+  void Initialize();
+
+  bool IsDualCoreMode() const { return m_separate_cpu_and_gpu_threads; }
+  bool IsMMUMode() const { return m_mmu_enabled; }
+
 private:
   System();
 
   struct Impl;
   std::unique_ptr<Impl> m_impl;
+
+  bool m_separate_cpu_and_gpu_threads = false;
+  bool m_mmu_enabled = false;
 };
 }  // namespace Core
diff --git a/Source/Core/DolphinQt/Settings/AdvancedPane.cpp b/Source/Core/DolphinQt/Settings/AdvancedPane.cpp
index 28f6a75030..bdea2ed2ba 100644
--- a/Source/Core/DolphinQt/Settings/AdvancedPane.cpp
+++ b/Source/Core/DolphinQt/Settings/AdvancedPane.cpp
@@ -178,7 +178,7 @@ void AdvancedPane::ConnectLayout()
           });
 
   connect(m_enable_mmu_checkbox, &QCheckBox::toggled, this,
-          [](bool checked) { SConfig::GetInstance().bMMU = checked; });
+          [](bool checked) { Config::SetBaseOrCurrent(Config::MAIN_MMU, checked); });
 
   m_cpu_clock_override_checkbox->setChecked(Config::Get(Config::MAIN_OVERCLOCK_ENABLE));
   connect(m_cpu_clock_override_checkbox, &QCheckBox::toggled, [this](bool enable_clock_override) {
@@ -243,7 +243,7 @@ void AdvancedPane::Update()
   }
   m_cpu_emulation_engine_combobox->setEnabled(!running);
 
-  m_enable_mmu_checkbox->setChecked(SConfig::GetInstance().bMMU);
+  m_enable_mmu_checkbox->setChecked(Config::Get(Config::MAIN_MMU));
   m_enable_mmu_checkbox->setEnabled(!running);
 
   QFont bf = font();
diff --git a/Source/Core/DolphinQt/Settings/GeneralPane.cpp b/Source/Core/DolphinQt/Settings/GeneralPane.cpp
index 05ea785484..e8ec3eeab0 100644
--- a/Source/Core/DolphinQt/Settings/GeneralPane.cpp
+++ b/Source/Core/DolphinQt/Settings/GeneralPane.cpp
@@ -252,7 +252,7 @@ void GeneralPane::LoadConfig()
 #if defined(USE_ANALYTICS) && USE_ANALYTICS
   m_checkbox_enable_analytics->setChecked(Settings::Instance().IsAnalyticsEnabled());
 #endif
-  m_checkbox_dualcore->setChecked(SConfig::GetInstance().bCPUThread);
+  m_checkbox_dualcore->setChecked(Config::Get(Config::MAIN_CPU_THREAD));
   m_checkbox_cheats->setChecked(Settings::Instance().GetCheatsEnabled());
   m_checkbox_override_region_settings->setChecked(
       Config::Get(Config::MAIN_OVERRIDE_REGION_SETTINGS));
@@ -263,7 +263,7 @@ void GeneralPane::LoadConfig()
   int selection = qRound(Config::Get(Config::MAIN_EMULATION_SPEED) * 10);
   if (selection < m_combobox_speedlimit->count())
     m_combobox_speedlimit->setCurrentIndex(selection);
-  m_checkbox_dualcore->setChecked(SConfig::GetInstance().bCPUThread);
+  m_checkbox_dualcore->setChecked(Config::Get(Config::MAIN_CPU_THREAD));
 
   const auto fallback = Settings::Instance().GetFallbackRegion();
 
@@ -346,7 +346,6 @@ void GeneralPane::OnSaveConfig()
   Settings::Instance().SetAnalyticsEnabled(m_checkbox_enable_analytics->isChecked());
   DolphinAnalytics::Instance().ReloadConfig();
 #endif
-  settings.bCPUThread = m_checkbox_dualcore->isChecked();
   Config::SetBaseOrCurrent(Config::MAIN_CPU_THREAD, m_checkbox_dualcore->isChecked());
   Settings::Instance().SetCheatsEnabled(m_checkbox_cheats->isChecked());
   Config::SetBaseOrCurrent(Config::MAIN_OVERRIDE_REGION_SETTINGS,
diff --git a/Source/Core/VideoCommon/CommandProcessor.cpp b/Source/Core/VideoCommon/CommandProcessor.cpp
index ddaa0e72a3..c80469f89d 100644
--- a/Source/Core/VideoCommon/CommandProcessor.cpp
+++ b/Source/Core/VideoCommon/CommandProcessor.cpp
@@ -17,6 +17,7 @@
 #include "Core/HW/GPFifo.h"
 #include "Core/HW/MMIO.h"
 #include "Core/HW/ProcessorInterface.h"
+#include "Core/System.h"
 #include "VideoCommon/Fifo.h"
 
 namespace CommandProcessor
@@ -42,7 +43,7 @@ static Common::Flag s_interrupt_waiting;
 
 static bool IsOnThread()
 {
-  return SConfig::GetInstance().bCPUThread;
+  return Core::System::GetInstance().IsDualCoreMode();
 }
 
 static void UpdateInterrupts_Wrapper(u64 userdata, s64 cyclesLate)
diff --git a/Source/Core/VideoCommon/Fifo.cpp b/Source/Core/VideoCommon/Fifo.cpp
index 624e98452e..9d558d056d 100644
--- a/Source/Core/VideoCommon/Fifo.cpp
+++ b/Source/Core/VideoCommon/Fifo.cpp
@@ -19,6 +19,7 @@
 #include "Core/CoreTiming.h"
 #include "Core/HW/Memmap.h"
 #include "Core/Host.h"
+#include "Core/System.h"
 
 #include "VideoCommon/AsyncRequests.h"
 #include "VideoCommon/CPMemory.h"
@@ -71,6 +72,20 @@ static std::atomic<int> s_sync_ticks;
 static bool s_syncing_suspended;
 static Common::Event s_sync_wakeup_event;
 
+static std::optional<size_t> s_config_callback_id = std::nullopt;
+static bool s_config_sync_gpu = false;
+static int s_config_sync_gpu_max_distance = 0;
+static int s_config_sync_gpu_min_distance = 0;
+static float s_config_sync_gpu_overclock = 0.0f;
+
+static void RefreshConfig()
+{
+  s_config_sync_gpu = Config::Get(Config::MAIN_SYNC_GPU);
+  s_config_sync_gpu_max_distance = Config::Get(Config::MAIN_SYNC_GPU_MAX_DISTANCE);
+  s_config_sync_gpu_min_distance = Config::Get(Config::MAIN_SYNC_GPU_MIN_DISTANCE);
+  s_config_sync_gpu_overclock = Config::Get(Config::MAIN_SYNC_GPU_OVERCLOCK);
+}
+
 void DoState(PointerWrap& p)
 {
   p.DoArray(s_video_buffer, FIFO_SIZE);
@@ -95,9 +110,7 @@ void PauseAndLock(bool doLock, bool unpauseOnUnlock)
     SyncGPU(SyncGPUReason::Other);
     EmulatorState(false);
 
-    const SConfig& param = SConfig::GetInstance();
-
-    if (!param.bCPUThread || s_use_deterministic_gpu_thread)
+    if (!Core::System::GetInstance().IsDualCoreMode() || s_use_deterministic_gpu_thread)
       return;
 
     s_gpu_mainloop.WaitYield(std::chrono::milliseconds(100), Host_YieldToUI);
@@ -111,10 +124,14 @@ void PauseAndLock(bool doLock, bool unpauseOnUnlock)
 
 void Init()
 {
+  if (!s_config_callback_id)
+    s_config_callback_id = Config::AddConfigChangedCallback(RefreshConfig);
+  RefreshConfig();
+
   // Padded so that SIMD overreads in the vertex loader are safe
   s_video_buffer = static_cast<u8*>(Common::AllocateMemoryPages(FIFO_SIZE + 4));
   ResetVideoBuffer();
-  if (SConfig::GetInstance().bCPUThread)
+  if (Core::System::GetInstance().IsDualCoreMode())
     s_gpu_mainloop.Prepare();
   s_sync_ticks.store(0);
 }
@@ -132,6 +149,12 @@ void Shutdown()
   s_video_buffer_seen_ptr = nullptr;
   s_fifo_aux_write_ptr = nullptr;
   s_fifo_aux_read_ptr = nullptr;
+
+  if (s_config_callback_id)
+  {
+    Config::RemoveConfigChangedCallback(*s_config_callback_id);
+    s_config_callback_id = std::nullopt;
+  }
 }
 
 // May be executed from any thread, even the graphics thread.
@@ -297,10 +320,8 @@ void RunGpuLoop()
   AsyncRequests::GetInstance()->SetEnable(true);
   AsyncRequests::GetInstance()->SetPassthrough(false);
 
-  const SConfig& param = SConfig::GetInstance();
-
   s_gpu_mainloop.Run(
-      [&param] {
+      [] {
         // Run events from the CPU thread.
         AsyncRequests::GetInstance()->PullEvents();
 
@@ -331,7 +352,7 @@ void RunGpuLoop()
                  fifo.bFF_GPReadEnable.load(std::memory_order_relaxed) &&
                  fifo.CPReadWriteDistance.load(std::memory_order_relaxed) && !AtBreakpoint())
           {
-            if (param.bSyncGPU && s_sync_ticks.load() < param.iSyncGpuMinDistance)
+            if (s_config_sync_gpu && s_sync_ticks.load() < s_config_sync_gpu_min_distance)
               break;
 
             u32 cyclesExecuted = 0;
@@ -363,12 +384,12 @@ void RunGpuLoop()
 
             CommandProcessor::SetCPStatusFromGPU();
 
-            if (param.bSyncGPU)
+            if (s_config_sync_gpu)
             {
-              cyclesExecuted = (int)(cyclesExecuted / param.fSyncGpuOverclock);
+              cyclesExecuted = (int)(cyclesExecuted / s_config_sync_gpu_overclock);
               int old = s_sync_ticks.fetch_sub(cyclesExecuted);
-              if (old >= param.iSyncGpuMaxDistance &&
-                  old - (int)cyclesExecuted < param.iSyncGpuMaxDistance)
+              if (old >= s_config_sync_gpu_max_distance &&
+                  old - (int)cyclesExecuted < s_config_sync_gpu_max_distance)
                 s_sync_wakeup_event.Set();
             }
 
@@ -383,7 +404,7 @@ void RunGpuLoop()
           if (s_sync_ticks.load() > 0)
           {
             int old = s_sync_ticks.exchange(0);
-            if (old >= param.iSyncGpuMaxDistance)
+            if (old >= s_config_sync_gpu_max_distance)
               s_sync_wakeup_event.Set();
           }
 
@@ -400,9 +421,7 @@ void RunGpuLoop()
 
 void FlushGpu()
 {
-  const SConfig& param = SConfig::GetInstance();
-
-  if (!param.bCPUThread || s_use_deterministic_gpu_thread)
+  if (!Core::System::GetInstance().IsDualCoreMode() || s_use_deterministic_gpu_thread)
     return;
 
   s_gpu_mainloop.Wait();
@@ -423,17 +442,16 @@ bool AtBreakpoint()
 
 void RunGpu()
 {
-  const SConfig& param = SConfig::GetInstance();
+  const bool is_dual_core = Core::System::GetInstance().IsDualCoreMode();
 
   // wake up GPU thread
-  if (param.bCPUThread && !s_use_deterministic_gpu_thread)
+  if (is_dual_core && !s_use_deterministic_gpu_thread)
   {
     s_gpu_mainloop.Wakeup();
   }
 
   // if the sync GPU callback is suspended, wake it up.
-  if (!SConfig::GetInstance().bCPUThread || s_use_deterministic_gpu_thread ||
-      SConfig::GetInstance().bSyncGPU)
+  if (!is_dual_core || s_use_deterministic_gpu_thread || s_config_sync_gpu)
   {
     if (s_syncing_suspended)
     {
@@ -447,7 +465,7 @@ static int RunGpuOnCpu(int ticks)
 {
   CommandProcessor::SCPFifoStruct& fifo = CommandProcessor::fifo;
   bool reset_simd_state = false;
-  int available_ticks = int(ticks * SConfig::GetInstance().fSyncGpuOverclock) + s_sync_ticks.load();
+  int available_ticks = int(ticks * s_config_sync_gpu_overclock) + s_sync_ticks.load();
   while (fifo.bFF_GPReadEnable.load(std::memory_order_relaxed) &&
          fifo.CPReadWriteDistance.load(std::memory_order_relaxed) && !AtBreakpoint() &&
          available_ticks >= 0)
@@ -508,7 +526,6 @@ void UpdateWantDeterminism(bool want)
 {
   // We are paused (or not running at all yet), so
   // it should be safe to change this.
-  const SConfig& param = SConfig::GetInstance();
   bool gpu_thread = false;
   switch (Config::GetGPUDeterminismMode())
   {
@@ -523,7 +540,7 @@ void UpdateWantDeterminism(bool want)
     break;
   }
 
-  gpu_thread = gpu_thread && param.bCPUThread;
+  gpu_thread = gpu_thread && Core::System::GetInstance().IsDualCoreMode();
 
   if (s_use_deterministic_gpu_thread != gpu_thread)
   {
@@ -550,8 +567,6 @@ bool UseDeterministicGPUThread()
  */
 static int WaitForGpuThread(int ticks)
 {
-  const SConfig& param = SConfig::GetInstance();
-
   int old = s_sync_ticks.fetch_add(ticks);
   int now = old + ticks;
 
@@ -560,15 +575,15 @@ static int WaitForGpuThread(int ticks)
     return -1;
 
   // Wakeup GPU
-  if (old < param.iSyncGpuMinDistance && now >= param.iSyncGpuMinDistance)
+  if (old < s_config_sync_gpu_min_distance && now >= s_config_sync_gpu_min_distance)
     RunGpu();
 
   // If the GPU is still sleeping, wait for a longer time
-  if (now < param.iSyncGpuMinDistance)
-    return GPU_TIME_SLOT_SIZE + param.iSyncGpuMinDistance - now;
+  if (now < s_config_sync_gpu_min_distance)
+    return GPU_TIME_SLOT_SIZE + s_config_sync_gpu_min_distance - now;
 
   // Wait for GPU
-  if (now >= param.iSyncGpuMaxDistance)
+  if (now >= s_config_sync_gpu_max_distance)
     s_sync_wakeup_event.Wait();
 
   return GPU_TIME_SLOT_SIZE;
@@ -579,11 +594,11 @@ static void SyncGPUCallback(u64 ticks, s64 cyclesLate)
   ticks += cyclesLate;
   int next = -1;
 
-  if (!SConfig::GetInstance().bCPUThread || s_use_deterministic_gpu_thread)
+  if (!Core::System::GetInstance().IsDualCoreMode() || s_use_deterministic_gpu_thread)
   {
     next = RunGpuOnCpu((int)ticks);
   }
-  else if (SConfig::GetInstance().bSyncGPU)
+  else if (s_config_sync_gpu)
   {
     next = WaitForGpuThread((int)ticks);
   }
@@ -597,9 +612,9 @@ void SyncGPUForRegisterAccess()
 {
   SyncGPU(SyncGPUReason::Other);
 
-  if (!SConfig::GetInstance().bCPUThread || s_use_deterministic_gpu_thread)
+  if (!Core::System::GetInstance().IsDualCoreMode() || s_use_deterministic_gpu_thread)
     RunGpuOnCpu(GPU_TIME_SLOT_SIZE);
-  else if (SConfig::GetInstance().bSyncGPU)
+  else if (s_config_sync_gpu)
     WaitForGpuThread(GPU_TIME_SLOT_SIZE);
 }
 
diff --git a/Source/Core/VideoCommon/PixelEngine.cpp b/Source/Core/VideoCommon/PixelEngine.cpp
index 747328b3c6..bdfaa599d5 100644
--- a/Source/Core/VideoCommon/PixelEngine.cpp
+++ b/Source/Core/VideoCommon/PixelEngine.cpp
@@ -10,11 +10,14 @@
 #include "Common/ChunkFile.h"
 #include "Common/CommonTypes.h"
 #include "Common/Logging/Log.h"
+
 #include "Core/ConfigManager.h"
 #include "Core/Core.h"
 #include "Core/CoreTiming.h"
 #include "Core/HW/MMIO.h"
 #include "Core/HW/ProcessorInterface.h"
+#include "Core/System.h"
+
 #include "VideoCommon/BoundingBox.h"
 #include "VideoCommon/Fifo.h"
 #include "VideoCommon/PerfQueryBase.h"
@@ -286,7 +289,7 @@ static void RaiseEvent(int cycles_into_future)
 
   CoreTiming::FromThread from = CoreTiming::FromThread::NON_CPU;
   s64 cycles = 0;  // we don't care about timings for dual core mode.
-  if (!SConfig::GetInstance().bCPUThread || Fifo::UseDeterministicGPUThread())
+  if (!Core::System::GetInstance().IsDualCoreMode() || Fifo::UseDeterministicGPUThread())
   {
     from = CoreTiming::FromThread::CPU;
 
diff --git a/Source/Core/VideoCommon/VideoBackendBase.cpp b/Source/Core/VideoCommon/VideoBackendBase.cpp
index 03d46b7ff6..b84f6f9b24 100644
--- a/Source/Core/VideoCommon/VideoBackendBase.cpp
+++ b/Source/Core/VideoCommon/VideoBackendBase.cpp
@@ -13,7 +13,6 @@
 
 #include "Common/ChunkFile.h"
 #include "Common/CommonTypes.h"
-#include "Common/Config/Config.h"
 #include "Common/Event.h"
 #include "Common/FileUtil.h"
 #include "Common/Logging/Log.h"
@@ -21,6 +20,7 @@
 #include "Core/Config/MainSettings.h"
 #include "Core/ConfigManager.h"
 #include "Core/Core.h"
+#include "Core/System.h"
 
 // TODO: ugly
 #ifdef _WIN32
@@ -289,7 +289,7 @@ void VideoBackendBase::PopulateBackendInfoFromUI()
 
 void VideoBackendBase::DoState(PointerWrap& p)
 {
-  if (!SConfig::GetInstance().bCPUThread)
+  if (!Core::System::GetInstance().IsDualCoreMode())
   {
     VideoCommon_DoState(p);
     return;