diff --git a/Source/Core/DolphinQt/Main.cpp b/Source/Core/DolphinQt/Main.cpp
index 317d12fefa..4b01bdcc27 100644
--- a/Source/Core/DolphinQt/Main.cpp
+++ b/Source/Core/DolphinQt/Main.cpp
@@ -257,8 +257,6 @@ int main(int argc, char* argv[])
 
     MainWindow win{std::move(boot), static_cast<const char*>(options.get("movie"))};
     Settings::Instance().SetCurrentUserStyle(Settings::Instance().GetCurrentUserStyle());
-    if (options.is_set("debugger"))
-      Settings::Instance().SetDebugModeEnabled(true);
     win.Show();
 
 #if defined(USE_ANALYTICS) && USE_ANALYTICS
diff --git a/Source/Core/UICommon/CommandLineParse.cpp b/Source/Core/UICommon/CommandLineParse.cpp
index 54093f219a..a37f0f2561 100644
--- a/Source/Core/UICommon/CommandLineParse.cpp
+++ b/Source/Core/UICommon/CommandLineParse.cpp
@@ -22,7 +22,7 @@ class CommandLineConfigLayerLoader final : public Config::ConfigLayerLoader
 {
 public:
   CommandLineConfigLayerLoader(const std::list<std::string>& args, const std::string& video_backend,
-                               const std::string& audio_backend, bool batch)
+                               const std::string& audio_backend, bool batch, bool debugger)
       : ConfigLayerLoader(Config::LayerType::CommandLine)
   {
     if (!video_backend.empty())
@@ -39,6 +39,9 @@ public:
     if (batch)
       m_values.emplace_back(Config::MAIN_RENDER_TO_MAIN.GetLocation(), ValueToString(false));
 
+    if (debugger)
+      m_values.emplace_back(Config::MAIN_ENABLE_DEBUGGING.GetLocation(), ValueToString(true));
+
     // Arguments are in the format of <System>.<Section>.<Key>=Value
     for (const auto& arg : args)
     {
@@ -134,7 +137,7 @@ static void AddConfigLayer(const optparse::Values& options)
   Config::AddLayer(std::make_unique<CommandLineConfigLayerLoader>(
       std::move(config_args), static_cast<const char*>(options.get("video_backend")),
       static_cast<const char*>(options.get("audio_emulation")),
-      static_cast<bool>(options.get("batch"))));
+      static_cast<bool>(options.get("batch")), static_cast<bool>(options.get("debugger"))));
 }
 
 optparse::Values& ParseArguments(optparse::OptionParser* parser, int argc, char** argv)