diff --git a/Source/Core/Core/ConfigManager.cpp b/Source/Core/Core/ConfigManager.cpp
index 22cb976620..0518a6d400 100644
--- a/Source/Core/Core/ConfigManager.cpp
+++ b/Source/Core/Core/ConfigManager.cpp
@@ -175,6 +175,7 @@ void SConfig::SaveInterfaceSettings(IniFile& ini)
   interface->Set("ThemeName", theme_name);
   interface->Set("PauseOnFocusLost", m_PauseOnFocusLost);
   interface->Set("DisableTooltips", m_DisableTooltips);
+  interface->Set("DebugModeEnabled", bEnableDebugging);
 }
 
 void SConfig::SaveDisplaySettings(IniFile& ini)
@@ -461,6 +462,7 @@ void SConfig::LoadInterfaceSettings(IniFile& ini)
   interface->Get("ThemeName", &theme_name, DEFAULT_THEME_DIR);
   interface->Get("PauseOnFocusLost", &m_PauseOnFocusLost, false);
   interface->Get("DisableTooltips", &m_DisableTooltips, false);
+  interface->Get("DebugModeEnabled", &bEnableDebugging, false);
 }
 
 void SConfig::LoadDisplaySettings(IniFile& ini)
diff --git a/Source/Core/DolphinQt2/Main.cpp b/Source/Core/DolphinQt2/Main.cpp
index 1c46d4403d..047618df5c 100644
--- a/Source/Core/DolphinQt2/Main.cpp
+++ b/Source/Core/DolphinQt2/Main.cpp
@@ -105,7 +105,6 @@ int main(int argc, char* argv[])
   UICommon::CreateDirectories();
   UICommon::Init();
   Resources::Init();
-  Settings::Instance().SetDebugModeEnabled(options.is_set("debugger"));
   Settings::Instance().SetBatchModeEnabled(options.is_set("batch"));
 
   // Hook up alerts from core
@@ -148,6 +147,8 @@ int main(int argc, char* argv[])
     DolphinAnalytics::Instance()->ReportDolphinStart("qt");
 
     MainWindow win{std::move(boot)};
+    if (options.is_set("debugger"))
+      Settings::Instance().SetDebugModeEnabled(true);
     win.show();
 
 #if defined(USE_ANALYTICS) && USE_ANALYTICS