diff --git a/Source/Core/Core/IOS/SDIO/SDIOSlot0.cpp b/Source/Core/Core/IOS/SDIO/SDIOSlot0.cpp
@@ -15,6 +15,7 @@
 #include "Common/Logging/Log.h"
 #include "Common/SDCardUtil.h"
 
+#include "Core/CPUThreadConfigCallback.h"
 #include "Core/Config/MainSettings.h"
 #include "Core/Config/SessionSettings.h"
 #include "Core/Core.h"
@@ -32,27 +33,23 @@ SDIOSlot0Device::SDIOSlot0Device(EmulationKernel& ios, const std::string& device
   if (!Config::Get(Config::MAIN_ALLOW_SD_WRITES))
     INFO_LOG_FMT(IOS_SD, "Writes to SD card disabled by user");
 
-  m_config_callback_id = Config::AddConfigChangedCallback([this] { RefreshConfig(); });
+  m_config_callback_id =
+      CPUThreadConfigCallback::AddConfigChangedCallback([this] { RefreshConfig(); });
   m_sd_card_inserted = Config::Get(Config::MAIN_WII_SD_CARD);
 }
 
 SDIOSlot0Device::~SDIOSlot0Device()
 {
-  Config::RemoveConfigChangedCallback(m_config_callback_id);
+  CPUThreadConfigCallback::RemoveConfigChangedCallback(m_config_callback_id);
 }
 
 void SDIOSlot0Device::RefreshConfig()
 {
-  if (m_sd_card_inserted != Config::Get(Config::MAIN_WII_SD_CARD))
+  const bool sd_card_inserted = Config::Get(Config::MAIN_WII_SD_CARD);
+  if (m_sd_card_inserted != sd_card_inserted)
   {
-    Core::RunAsCPUThread([this] {
-      const bool sd_card_inserted = Config::Get(Config::MAIN_WII_SD_CARD);
-      if (m_sd_card_inserted != sd_card_inserted)
-      {
-        m_sd_card_inserted = sd_card_inserted;
-        EventNotify();
-      }
-    });
+    m_sd_card_inserted = sd_card_inserted;
+    EventNotify();
   }
 }
 

diff --git a/Source/Core/Core/IOS/SDIO/SDIOSlot0.h b/Source/Core/Core/IOS/SDIO/SDIOSlot0.h
@@ -10,6 +10,7 @@
 
 #include "Common/CommonTypes.h"
 #include "Common/IOFile.h"
+#include "Core/CPUThreadConfigCallback.h"
 #include "Core/IOS/Device.h"
 #include "Core/IOS/IOS.h"
 
@@ -166,7 +167,7 @@ class SDIOSlot0Device : public EmulationDevice
 
   File::IOFile m_card;
 
-  size_t m_config_callback_id;
+  CPUThreadConfigCallback::ConfigChangedCallbackID m_config_callback_id;
   bool m_sd_card_inserted = false;
 };
 }  // namespace IOS::HLE
diff --git a/Source/Core/Core/PowerPC/JitCommon/JitBase.cpp b/Source/Core/Core/PowerPC/JitCommon/JitBase.cpp
@@ -7,6 +7,8 @@
 #include "Common/CommonTypes.h"
 #include "Common/MemoryUtil.h"
 #include "Common/Thread.h"
+
+#include "Core/CPUThreadConfigCallback.h"
 #include "Core/Config/MainSettings.h"
 #include "Core/ConfigManager.h"
 #include "Core/Core.h"
@@ -64,14 +66,14 @@ JitBase::JitBase(Core::System& system)
     : m_code_buffer(code_buffer_size), m_system(system), m_ppc_state(system.GetPPCState()),
       m_mmu(system.GetMMU())
 {
-  m_registered_config_callback_id = Config::AddConfigChangedCallback(
-      [this] { Core::RunAsCPUThread([this] { RefreshConfig(); }); });
+  m_registered_config_callback_id =
+      CPUThreadConfigCallback::AddConfigChangedCallback([this] { RefreshConfig(); });
   RefreshConfig();
 }
 
 JitBase::~JitBase()
 {
-  Config::RemoveConfigChangedCallback(m_registered_config_callback_id);
+  CPUThreadConfigCallback::RemoveConfigChangedCallback(m_registered_config_callback_id);
 }
 
 void JitBase::RefreshConfig()

diff --git a/Source/Core/Core/PowerPC/JitCommon/JitBase.h b/Source/Core/Core/PowerPC/JitCommon/JitBase.h
@@ -10,6 +10,7 @@
 #include "Common/BitSet.h"
 #include "Common/CommonTypes.h"
 #include "Common/x64Emitter.h"
+#include "Core/CPUThreadConfigCallback.h"
 #include "Core/ConfigManager.h"
 #include "Core/MachineContext.h"
 #include "Core/PowerPC/CPUCoreBase.h"
@@ -129,7 +130,7 @@ class JitBase : public CPUCoreBase
   PPCAnalyst::CodeBuffer m_code_buffer;
   PPCAnalyst::PPCAnalyzer analyzer;
 
-  size_t m_registered_config_callback_id;
+  CPUThreadConfigCallback::ConfigChangedCallbackID m_registered_config_callback_id;
   bool bJITOff = false;
   bool bJITLoadStoreOff = false;
   bool bJITLoadStorelXzOff = false;

diff --git a/Source/Core/Core/PowerPC/PPCCache.h b/Source/Core/Core/PowerPC/PPCCache.h
@@ -8,6 +8,7 @@
 #include <vector>
 
 #include "Common/CommonTypes.h"
+#include "Common/Config/Config.h"
 
 class PointerWrap;
 
@@ -61,7 +62,7 @@ struct Cache
 
 struct InstructionCache : public Cache
 {
-  std::optional<size_t> m_config_callback_id = std::nullopt;
+  std::optional<Config::ConfigChangedCallbackID> m_config_callback_id = std::nullopt;
 
   bool m_disable_icache = false;
 

diff --git a/Source/Core/DolphinLib.props b/Source/Core/DolphinLib.props
@@ -191,6 +191,7 @@
     <ClInclude Include="Core\ConfigManager.h" />
     <ClInclude Include="Core\Core.h" />
     <ClInclude Include="Core\CoreTiming.h" />
+    <ClInclude Include="Core\CPUThreadConfigCallback.h" />
     <ClInclude Include="Core\Debugger\CodeTrace.h" />
     <ClInclude Include="Core\Debugger\DebugInterface.h" />
     <ClInclude Include="Core\Debugger\Debugger_SymbolMap.h" />
@@ -837,6 +838,7 @@
     <ClCompile Include="Core\ConfigManager.cpp" />
     <ClCompile Include="Core\Core.cpp" />
     <ClCompile Include="Core\CoreTiming.cpp" />
+    <ClCompile Include="Core\CPUThreadConfigCallback.cpp" />
     <ClCompile Include="Core\Debugger\CodeTrace.cpp" />
     <ClCompile Include="Core\Debugger\Debugger_SymbolMap.cpp" />
     <ClCompile Include="Core\Debugger\Dump.cpp" />

diff --git a/Source/Core/InputCommon/ControllerInterface/DualShockUDPClient/DualShockUDPClient.cpp b/Source/Core/InputCommon/ControllerInterface/DualShockUDPClient/DualShockUDPClient.cpp
@@ -219,7 +219,7 @@ class InputBackend final : public ciface::InputBackend
   SteadyClock::time_point m_next_listports_time;
   std::thread m_hotplug_thread;
   Common::Flag m_hotplug_thread_running;
-  std::size_t m_config_change_callback_id;
+  Config::ConfigChangedCallbackID m_config_change_callback_id;
 };
 
 std::unique_ptr<ciface::InputBackend> CreateInputBackend(ControllerInterface* controller_interface)

diff --git a/Source/Core/InputCommon/GCAdapter.cpp b/Source/Core/InputCommon/GCAdapter.cpp
@@ -23,6 +23,7 @@
 #endif
 
 #include "Common/BitUtils.h"
+#include "Common/Config/Config.h"
 #include "Common/Event.h"
 #include "Common/Flag.h"
 #include "Common/Logging/Log.h"
@@ -158,7 +159,7 @@ static u8 s_endpoint_out = 0;
 
 static u64 s_last_init = 0;
 
-static std::optional<size_t> s_config_callback_id = std::nullopt;
+static std::optional<Config::ConfigChangedCallbackID> s_config_callback_id = std::nullopt;
 
 static bool s_is_adapter_wanted = false;
 static std::array<bool, SerialInterface::MAX_SI_CHANNELS> s_config_rumble_enabled{};

diff --git a/Source/Core/UICommon/UICommon.cpp b/Source/Core/UICommon/UICommon.cpp
@@ -62,7 +62,7 @@
 
 namespace UICommon
 {
-static size_t s_config_changed_callback_id;
+static Config::ConfigChangedCallbackID s_config_changed_callback_id;
 
 static void CreateDumpPath(std::string path)
 {

diff --git a/Source/Core/VideoCommon/Fifo.h b/Source/Core/VideoCommon/Fifo.h
@@ -9,6 +9,7 @@
 
 #include "Common/BlockingLoop.h"
 #include "Common/CommonTypes.h"
+#include "Common/Config/Config.h"
 #include "Common/Event.h"
 #include "Common/Flag.h"
 
@@ -121,7 +122,7 @@ class FifoManager final
   bool m_syncing_suspended = false;
   Common::Event m_sync_wakeup_event;
 
-  std::optional<size_t> m_config_callback_id = std::nullopt;
+  std::optional<Config::ConfigChangedCallbackID> m_config_callback_id = std::nullopt;
   bool m_config_sync_gpu = false;
   int m_config_sync_gpu_max_distance = 0;
   int m_config_sync_gpu_min_distance = 0;

diff --git a/Source/Core/VideoCommon/VideoConfig.cpp b/Source/Core/VideoCommon/VideoConfig.cpp
@@ -9,6 +9,7 @@
 #include "Common/CommonTypes.h"
 #include "Common/StringUtil.h"
 
+#include "Core/CPUThreadConfigCallback.h"
 #include "Core/Config/GraphicsSettings.h"
 #include "Core/Config/MainSettings.h"
 #include "Core/ConfigManager.h"
@@ -19,6 +20,7 @@
 #include "VideoCommon/AbstractGfx.h"
 #include "VideoCommon/BPFunctions.h"
 #include "VideoCommon/DriverDetails.h"
+#include "VideoCommon/Fifo.h"
 #include "VideoCommon/FramebufferManager.h"
 #include "VideoCommon/FreeLookCamera.h"
 #include "VideoCommon/GraphicsModSystem/Config/GraphicsMod.h"
@@ -57,14 +59,21 @@ void VideoConfig::Refresh()
   {
     // There was a race condition between the video thread and the host thread here, if
     // corrections need to be made by VerifyValidity(). Briefly, the config will contain
-    // invalid values. Instead, pause emulation first, which will flush the video thread,
-    // update the config and correct it, then resume emulation, after which the video
-    // thread will detect the config has changed and act accordingly.
-    Config::AddConfigChangedCallback([]() {
-      Core::RunAsCPUThread([]() {
-        g_Config.Refresh();
-        g_Config.VerifyValidity();
-      });
+    // invalid values. Instead, pause the video thread first, update the config and correct
+    // it, then resume emulation, after which the video thread will detect the config has
+    // changed and act accordingly.
+    CPUThreadConfigCallback::AddConfigChangedCallback([]() {
+      auto& system = Core::System::GetInstance();
+
+      const bool lock_gpu_thread = Core::IsRunningAndStarted();
+      if (lock_gpu_thread)
+        system.GetFifo().PauseAndLock(system, true, false);
+
+      g_Config.Refresh();
+      g_Config.VerifyValidity();
+
+      if (lock_gpu_thread)
+        system.GetFifo().PauseAndLock(system, false, true);
     });
     s_has_registered_callback = true;
   }

diff --git a/Source/UnitTests/Core/PageFaultTest.cpp b/Source/UnitTests/Core/PageFaultTest.cpp
@@ -5,7 +5,9 @@
 #include <fmt/format.h>
 
 #include "Common/CommonTypes.h"
+#include "Common/ScopeGuard.h"
 #include "Common/Timer.h"
+#include "Core/Core.h"
 #include "Core/MemTools.h"
 #include "Core/PowerPC/JitCommon/JitBase.h"
 #include "Core/PowerPC/JitInterface.h"
@@ -75,6 +77,9 @@ TEST(PageFault, PageFault)
   EXPECT_NE(data, nullptr);
   Common::WriteProtectMemory(data, PAGE_GRAN, false);
 
+  Core::DeclareAsCPUThread();
+  Common::ScopeGuard cpu_thread_guard([] { Core::UndeclareAsCPUThread(); });
+
   auto& system = Core::System::GetInstance();
   auto unique_pfjit = std::make_unique<PageFaultFakeJit>(system);
   auto& pfjit = *unique_pfjit;

diff --git a/Source/UnitTests/Core/PowerPC/Jit64Common/ConvertDoubleToSingle.cpp b/Source/UnitTests/Core/PowerPC/Jit64Common/ConvertDoubleToSingle.cpp
@@ -5,7 +5,9 @@
 #include <tuple>
 
 #include "Common/CommonTypes.h"
+#include "Common/ScopeGuard.h"
 #include "Common/x64ABI.h"
+#include "Core/Core.h"
 #include "Core/PowerPC/Gekko.h"
 #include "Core/PowerPC/Interpreter/Interpreter_FPUtils.h"
 #include "Core/PowerPC/Jit64/Jit.h"
@@ -52,6 +54,9 @@ class TestCommonAsmRoutines : public CommonAsmRoutines
 
 TEST(Jit64, ConvertDoubleToSingle)
 {
+  Core::DeclareAsCPUThread();
+  Common::ScopeGuard cpu_thread_guard([] { Core::UndeclareAsCPUThread(); });
+
   TestCommonAsmRoutines routines(Core::System::GetInstance());
 
   for (const u64 input : double_test_values)

diff --git a/Source/UnitTests/Core/PowerPC/Jit64Common/Frsqrte.cpp b/Source/UnitTests/Core/PowerPC/Jit64Common/Frsqrte.cpp
@@ -6,7 +6,9 @@
 #include "Common/BitUtils.h"
 #include "Common/CommonTypes.h"
 #include "Common/FloatUtils.h"
+#include "Common/ScopeGuard.h"
 #include "Common/x64ABI.h"
+#include "Core/Core.h"
 #include "Core/PowerPC/Gekko.h"
 #include "Core/PowerPC/Jit64/Jit.h"
 #include "Core/PowerPC/Jit64Common/Jit64AsmCommon.h"
@@ -59,6 +61,9 @@ class TestCommonAsmRoutines : public CommonAsmRoutines
 
 TEST(Jit64, Frsqrte)
 {
+  Core::DeclareAsCPUThread();
+  Common::ScopeGuard cpu_thread_guard([] { Core::UndeclareAsCPUThread(); });
+
   TestCommonAsmRoutines routines(Core::System::GetInstance());
 
   UReg_FPSCR fpscr;

diff --git a/Source/UnitTests/Core/PowerPC/JitArm64/ConvertSingleDouble.cpp b/Source/UnitTests/Core/PowerPC/JitArm64/ConvertSingleDouble.cpp
@@ -7,6 +7,8 @@
 #include "Common/BitUtils.h"
 #include "Common/CommonTypes.h"
 #include "Common/FPURoundMode.h"
+#include "Common/ScopeGuard.h"
+#include "Core/Core.h"
 #include "Core/PowerPC/Interpreter/Interpreter_FPUtils.h"
 #include "Core/PowerPC/JitArm64/Jit.h"
 #include "Core/System.h"
@@ -120,6 +122,9 @@ class TestConversion : private JitArm64
 
 TEST(JitArm64, ConvertDoubleToSingle)
 {
+  Core::DeclareAsCPUThread();
+  Common::ScopeGuard cpu_thread_guard([] { Core::UndeclareAsCPUThread(); });
+
   TestConversion test(Core::System::GetInstance());
 
   for (const u64 input : double_test_values)
@@ -155,6 +160,9 @@ TEST(JitArm64, ConvertDoubleToSingle)
 
 TEST(JitArm64, ConvertSingleToDouble)
 {
+  Core::DeclareAsCPUThread();
+  Common::ScopeGuard cpu_thread_guard([] { Core::UndeclareAsCPUThread(); });
+
   TestConversion test(Core::System::GetInstance());
 
   for (const u32 input : single_test_values)

diff --git a/Source/UnitTests/Core/PowerPC/JitArm64/FPRF.cpp b/Source/UnitTests/Core/PowerPC/JitArm64/FPRF.cpp
@@ -7,6 +7,8 @@
 #include "Common/Arm64Emitter.h"
 #include "Common/BitUtils.h"
 #include "Common/CommonTypes.h"
+#include "Common/ScopeGuard.h"
+#include "Core/Core.h"
 #include "Core/PowerPC/Interpreter/Interpreter_FPUtils.h"
 #include "Core/PowerPC/JitArm64/Jit.h"
 #include "Core/PowerPC/PowerPC.h"
@@ -70,6 +72,9 @@ static u32 RunUpdateFPRF(PowerPC::PowerPCState& ppc_state, const std::function<v
 
 TEST(JitArm64, FPRF)
 {
+  Core::DeclareAsCPUThread();
+  Common::ScopeGuard cpu_thread_guard([] { Core::UndeclareAsCPUThread(); });
+
   auto& system = Core::System::GetInstance();
   auto& ppc_state = system.GetPPCState();
   TestFPRF test(system);

diff --git a/Source/UnitTests/Core/PowerPC/JitArm64/Fres.cpp b/Source/UnitTests/Core/PowerPC/JitArm64/Fres.cpp
@@ -6,6 +6,8 @@
 #include "Common/Arm64Emitter.h"
 #include "Common/BitUtils.h"
 #include "Common/CommonTypes.h"
+#include "Common/ScopeGuard.h"
+#include "Core/Core.h"
 #include "Core/PowerPC/Interpreter/Interpreter_FPUtils.h"
 #include "Core/PowerPC/JitArm64/Jit.h"
 #include "Core/PowerPC/PowerPC.h"
@@ -51,6 +53,9 @@ class TestFres : public JitArm64
 
 TEST(JitArm64, Fres)
 {
+  Core::DeclareAsCPUThread();
+  Common::ScopeGuard cpu_thread_guard([] { Core::UndeclareAsCPUThread(); });
+
   TestFres test(Core::System::GetInstance());
 
   for (const u64 ivalue : double_test_values)

diff --git a/Source/UnitTests/Core/PowerPC/JitArm64/Frsqrte.cpp b/Source/UnitTests/Core/PowerPC/JitArm64/Frsqrte.cpp
@@ -6,6 +6,8 @@
 #include "Common/Arm64Emitter.h"
 #include "Common/BitUtils.h"
 #include "Common/CommonTypes.h"
+#include "Common/ScopeGuard.h"
+#include "Core/Core.h"
 #include "Core/PowerPC/Interpreter/Interpreter_FPUtils.h"
 #include "Core/PowerPC/JitArm64/Jit.h"
 #include "Core/PowerPC/PowerPC.h"
@@ -51,6 +53,9 @@ class TestFrsqrte : public JitArm64
 
 TEST(JitArm64, Frsqrte)
 {
+  Core::DeclareAsCPUThread();
+  Common::ScopeGuard cpu_thread_guard([] { Core::UndeclareAsCPUThread(); });
+
   TestFrsqrte test(Core::System::GetInstance());
 
   for (const u64 ivalue : double_test_values)