diff --git a/Source/Core/DolphinWX/Debugger/CodeWindow.cpp b/Source/Core/DolphinWX/Debugger/CodeWindow.cpp
index 7c4c6de534..4f14da7302 100644
--- a/Source/Core/DolphinWX/Debugger/CodeWindow.cpp
+++ b/Source/Core/DolphinWX/Debugger/CodeWindow.cpp
@@ -480,48 +480,50 @@ void CCodeWindow::UpdateCallstack()
 // CPU Mode and JIT Menu
 void CCodeWindow::OnCPUMode(wxCommandEvent& event)
 {
-  switch (event.GetId())
-  {
-  case IDM_INTERPRETER:
-    PowerPC::SetMode(event.IsChecked() ? PowerPC::CoreMode::Interpreter : PowerPC::CoreMode::JIT);
-    break;
-  case IDM_JIT_OFF:
-    SConfig::GetInstance().bJITOff = event.IsChecked();
-    break;
-  case IDM_JIT_LS_OFF:
-    SConfig::GetInstance().bJITLoadStoreOff = event.IsChecked();
-    break;
-  case IDM_JIT_LSLXZ_OFF:
-    SConfig::GetInstance().bJITLoadStorelXzOff = event.IsChecked();
-    break;
-  case IDM_JIT_LSLWZ_OFF:
-    SConfig::GetInstance().bJITLoadStorelwzOff = event.IsChecked();
-    break;
-  case IDM_JIT_LSLBZX_OFF:
-    SConfig::GetInstance().bJITLoadStorelbzxOff = event.IsChecked();
-    break;
-  case IDM_JIT_LSF_OFF:
-    SConfig::GetInstance().bJITLoadStoreFloatingOff = event.IsChecked();
-    break;
-  case IDM_JIT_LSP_OFF:
-    SConfig::GetInstance().bJITLoadStorePairedOff = event.IsChecked();
-    break;
-  case IDM_JIT_FP_OFF:
-    SConfig::GetInstance().bJITFloatingPointOff = event.IsChecked();
-    break;
-  case IDM_JIT_I_OFF:
-    SConfig::GetInstance().bJITIntegerOff = event.IsChecked();
-    break;
-  case IDM_JIT_P_OFF:
-    SConfig::GetInstance().bJITPairedOff = event.IsChecked();
-    break;
-  case IDM_JIT_SR_OFF:
-    SConfig::GetInstance().bJITSystemRegistersOff = event.IsChecked();
-    break;
-  }
+  Core::RunAsCPUThread([&event] {
+    switch (event.GetId())
+    {
+    case IDM_INTERPRETER:
+      PowerPC::SetMode(event.IsChecked() ? PowerPC::CoreMode::Interpreter : PowerPC::CoreMode::JIT);
+      break;
+    case IDM_JIT_OFF:
+      SConfig::GetInstance().bJITOff = event.IsChecked();
+      break;
+    case IDM_JIT_LS_OFF:
+      SConfig::GetInstance().bJITLoadStoreOff = event.IsChecked();
+      break;
+    case IDM_JIT_LSLXZ_OFF:
+      SConfig::GetInstance().bJITLoadStorelXzOff = event.IsChecked();
+      break;
+    case IDM_JIT_LSLWZ_OFF:
+      SConfig::GetInstance().bJITLoadStorelwzOff = event.IsChecked();
+      break;
+    case IDM_JIT_LSLBZX_OFF:
+      SConfig::GetInstance().bJITLoadStorelbzxOff = event.IsChecked();
+      break;
+    case IDM_JIT_LSF_OFF:
+      SConfig::GetInstance().bJITLoadStoreFloatingOff = event.IsChecked();
+      break;
+    case IDM_JIT_LSP_OFF:
+      SConfig::GetInstance().bJITLoadStorePairedOff = event.IsChecked();
+      break;
+    case IDM_JIT_FP_OFF:
+      SConfig::GetInstance().bJITFloatingPointOff = event.IsChecked();
+      break;
+    case IDM_JIT_I_OFF:
+      SConfig::GetInstance().bJITIntegerOff = event.IsChecked();
+      break;
+    case IDM_JIT_P_OFF:
+      SConfig::GetInstance().bJITPairedOff = event.IsChecked();
+      break;
+    case IDM_JIT_SR_OFF:
+      SConfig::GetInstance().bJITSystemRegistersOff = event.IsChecked();
+      break;
+    }
 
-  // Clear the JIT cache to enable these changes
-  JitInterface::ClearCache();
+    // Clear the JIT cache to enable these changes
+    JitInterface::ClearCache();
+  });
 }
 
 void CCodeWindow::OnJitMenu(wxCommandEvent& event)
@@ -533,7 +535,7 @@ void CCodeWindow::OnJitMenu(wxCommandEvent& event)
     break;
 
   case IDM_CLEAR_CODE_CACHE:
-    JitInterface::ClearCache();
+    Core::RunAsCPUThread(JitInterface::ClearCache);
     break;
 
   case IDM_SEARCH_INSTRUCTION:
diff --git a/Source/Core/DolphinWX/FrameTools.cpp b/Source/Core/DolphinWX/FrameTools.cpp
index c98297a421..77d7fe00d4 100644
--- a/Source/Core/DolphinWX/FrameTools.cpp
+++ b/Source/Core/DolphinWX/FrameTools.cpp
@@ -237,18 +237,18 @@ void CFrame::BindDebuggerMenuBarUpdateEvents()
 
   Bind(wxEVT_UPDATE_UI, &CFrame::OnUpdateInterpreterMenuItem, this, IDM_INTERPRETER);
 
-  Bind(wxEVT_UPDATE_UI, &WxEventUtils::OnEnableIfCorePaused, IDM_JIT_OFF);
-  Bind(wxEVT_UPDATE_UI, &WxEventUtils::OnEnableIfCorePaused, IDM_JIT_LS_OFF);
-  Bind(wxEVT_UPDATE_UI, &WxEventUtils::OnEnableIfCorePaused, IDM_JIT_LSLXZ_OFF);
-  Bind(wxEVT_UPDATE_UI, &WxEventUtils::OnEnableIfCorePaused, IDM_JIT_LSLWZ_OFF);
-  Bind(wxEVT_UPDATE_UI, &WxEventUtils::OnEnableIfCorePaused, IDM_JIT_LSLBZX_OFF);
-  Bind(wxEVT_UPDATE_UI, &WxEventUtils::OnEnableIfCorePaused, IDM_JIT_LSF_OFF);
-  Bind(wxEVT_UPDATE_UI, &WxEventUtils::OnEnableIfCorePaused, IDM_JIT_LSP_OFF);
-  Bind(wxEVT_UPDATE_UI, &WxEventUtils::OnEnableIfCorePaused, IDM_JIT_FP_OFF);
-  Bind(wxEVT_UPDATE_UI, &WxEventUtils::OnEnableIfCorePaused, IDM_JIT_I_OFF);
-  Bind(wxEVT_UPDATE_UI, &WxEventUtils::OnEnableIfCorePaused, IDM_JIT_P_OFF);
-  Bind(wxEVT_UPDATE_UI, &WxEventUtils::OnEnableIfCorePaused, IDM_JIT_SR_OFF);
-  Bind(wxEVT_UPDATE_UI, &WxEventUtils::OnEnableIfCorePaused, IDM_CLEAR_CODE_CACHE);
+  Bind(wxEVT_UPDATE_UI, &WxEventUtils::OnEnableIfCoreRunning, IDM_JIT_OFF);
+  Bind(wxEVT_UPDATE_UI, &WxEventUtils::OnEnableIfCoreRunning, IDM_JIT_LS_OFF);
+  Bind(wxEVT_UPDATE_UI, &WxEventUtils::OnEnableIfCoreRunning, IDM_JIT_LSLXZ_OFF);
+  Bind(wxEVT_UPDATE_UI, &WxEventUtils::OnEnableIfCoreRunning, IDM_JIT_LSLWZ_OFF);
+  Bind(wxEVT_UPDATE_UI, &WxEventUtils::OnEnableIfCoreRunning, IDM_JIT_LSLBZX_OFF);
+  Bind(wxEVT_UPDATE_UI, &WxEventUtils::OnEnableIfCoreRunning, IDM_JIT_LSF_OFF);
+  Bind(wxEVT_UPDATE_UI, &WxEventUtils::OnEnableIfCoreRunning, IDM_JIT_LSP_OFF);
+  Bind(wxEVT_UPDATE_UI, &WxEventUtils::OnEnableIfCoreRunning, IDM_JIT_FP_OFF);
+  Bind(wxEVT_UPDATE_UI, &WxEventUtils::OnEnableIfCoreRunning, IDM_JIT_I_OFF);
+  Bind(wxEVT_UPDATE_UI, &WxEventUtils::OnEnableIfCoreRunning, IDM_JIT_P_OFF);
+  Bind(wxEVT_UPDATE_UI, &WxEventUtils::OnEnableIfCoreRunning, IDM_JIT_SR_OFF);
+  Bind(wxEVT_UPDATE_UI, &WxEventUtils::OnEnableIfCoreRunning, IDM_CLEAR_CODE_CACHE);
 
   Bind(wxEVT_UPDATE_UI, &WxEventUtils::OnEnableIfCoreInitialized, IDM_SEARCH_INSTRUCTION);
   Bind(wxEVT_UPDATE_UI, &WxEventUtils::OnEnableIfCoreInitialized, IDM_CLEAR_SYMBOLS);
@@ -1111,7 +1111,7 @@ void CFrame::OnRescanGameList(wxCommandEvent& WXUNUSED(event))
 
 void CFrame::OnUpdateInterpreterMenuItem(wxUpdateUIEvent& event)
 {
-  WxEventUtils::OnEnableIfCorePaused(event);
+  WxEventUtils::OnEnableIfCoreRunning(event);
 
   if (GetMenuBar()->FindItem(IDM_INTERPRETER)->IsChecked())
     return;