diff --git a/Source/Core/Core/BootManager.cpp b/Source/Core/Core/BootManager.cpp
index b58818cc29..422bd2dede 100644
--- a/Source/Core/Core/BootManager.cpp
+++ b/Source/Core/Core/BootManager.cpp
@@ -70,7 +70,6 @@ public:
 
 private:
   bool valid = false;
-  bool bMMU = false;
   bool bSyncGPU = false;
   int iSyncGpuMaxDistance = 0;
   int iSyncGpuMinDistance = 0;
@@ -82,7 +81,6 @@ void ConfigCache::SaveConfig(const SConfig& config)
 {
   valid = true;
 
-  bMMU = config.bMMU;
   bSyncGPU = config.bSyncGPU;
   iSyncGpuMaxDistance = config.iSyncGpuMaxDistance;
   iSyncGpuMinDistance = config.iSyncGpuMinDistance;
@@ -102,7 +100,6 @@ void ConfigCache::RestoreConfig(SConfig* config)
 
   valid = false;
 
-  config->bMMU = bMMU;
   config->bSyncGPU = bSyncGPU;
   config->iSyncGpuMaxDistance = iSyncGpuMaxDistance;
   config->iSyncGpuMinDistance = iSyncGpuMinDistance;
@@ -144,7 +141,6 @@ bool BootCore(std::unique_ptr<BootParameters> boot, const WindowSystemInfo& wsi)
     IniFile::Section* core_section = game_ini.GetOrCreateSection("Core");
     IniFile::Section* controls_section = game_ini.GetOrCreateSection("Controls");
 
-    core_section->Get("MMU", &StartUp.bMMU, StartUp.bMMU);
     core_section->Get("SyncGPU", &StartUp.bSyncGPU, StartUp.bSyncGPU);
 
     // Wii settings
@@ -204,7 +200,6 @@ bool BootCore(std::unique_ptr<BootParameters> boot, const WindowSystemInfo& wsi)
     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
   {
diff --git a/Source/Core/Core/ConfigLoaders/IsSettingSaveable.cpp b/Source/Core/Core/ConfigLoaders/IsSettingSaveable.cpp
index fa2937363b..4b6ea5a9c4 100644
--- a/Source/Core/Core/ConfigLoaders/IsSettingSaveable.cpp
+++ b/Source/Core/Core/ConfigLoaders/IsSettingSaveable.cpp
@@ -118,6 +118,7 @@ bool IsSettingSaveable(const Config::Location& config_location)
       &Config::GetInfoForSIDevice(2).GetLocation(),
       &Config::GetInfoForSIDevice(3).GetLocation(),
       &Config::MAIN_CPU_THREAD.GetLocation(),
+      &Config::MAIN_MMU.GetLocation(),
 
       // UI.General
 
diff --git a/Source/Core/Core/ConfigManager.cpp b/Source/Core/Core/ConfigManager.cpp
index bfbc84d38b..5e4e883033 100644
--- a/Source/Core/Core/ConfigManager.cpp
+++ b/Source/Core/Core/ConfigManager.cpp
@@ -103,7 +103,6 @@ void SConfig::SaveCoreSettings(IniFile& ini)
   core->Set("SyncGpuMaxDistance", iSyncGpuMaxDistance);
   core->Set("SyncGpuMinDistance", iSyncGpuMinDistance);
   core->Set("SyncGpuOverclock", fSyncGpuOverclock);
-  core->Set("MMU", bMMU);
 }
 
 void SConfig::LoadSettings()
@@ -121,7 +120,6 @@ void SConfig::LoadCoreSettings(IniFile& ini)
 {
   IniFile::Section* core = ini.GetOrCreateSection("Core");
 
-  core->Get("MMU", &bMMU, bMMU);
   core->Get("BBDumpPort", &iBBDumpPort, -1);
   core->Get("SyncGPU", &bSyncGPU, false);
   core->Get("SyncGpuMaxDistance", &iSyncGpuMaxDistance, 200000);
@@ -242,7 +240,6 @@ void SConfig::LoadDefaults()
   bAutomaticStart = false;
   bBootToPause = false;
 
-  bMMU = false;
   iBBDumpPort = -1;
   bSyncGPU = false;
   bWii = false;
diff --git a/Source/Core/Core/ConfigManager.h b/Source/Core/Core/ConfigManager.h
index 4f965da655..a86c7189eb 100644
--- a/Source/Core/Core/ConfigManager.h
+++ b/Source/Core/Core/ConfigManager.h
@@ -58,7 +58,6 @@ struct SConfig
 
   bool bCopyWiiSaveNetplay = true;
 
-  bool bMMU = false;
   int iBBDumpPort = 0;
 
   bool bSyncGPU = false;
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/PowerPC/JitArm64/Jit.cpp b/Source/Core/Core/PowerPC/JitArm64/Jit.cpp
index c701f160c6..b19fea4598 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 b665d6f6c7..e7e14ea91e 100644
--- a/Source/Core/Core/System.cpp
+++ b/Source/Core/Core/System.cpp
@@ -20,5 +20,6 @@ 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 7b045d2a80..14d48ce477 100644
--- a/Source/Core/Core/System.h
+++ b/Source/Core/Core/System.h
@@ -29,6 +29,7 @@ public:
   void Initialize();
 
   bool IsDualCoreMode() const { return m_separate_cpu_and_gpu_threads; }
+  bool IsMMUMode() const { return m_mmu_enabled; }
 
 private:
   System();
@@ -37,5 +38,6 @@ private:
   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();