diff --git a/Source/Core/Common/Config/Config.cpp b/Source/Core/Common/Config/Config.cpp
index bcfb9a2619..5c69f27365 100644
--- a/Source/Core/Common/Config/Config.cpp
+++ b/Source/Core/Common/Config/Config.cpp
@@ -91,6 +91,9 @@ void Save()
 
 void Init()
 {
+  // These layers contain temporary values
+  s_layers[LayerType::CommandLine] = std::make_unique<Layer>(LayerType::CommandLine);
+  ClearCurrentRunLayer();
   // This layer always has to exist
   s_layers[LayerType::Meta] = std::make_unique<RecursiveLayer>();
 }
@@ -101,6 +104,11 @@ void Shutdown()
   s_callbacks.clear();
 }
 
+void ClearCurrentRunLayer()
+{
+  s_layers[LayerType::CurrentRun] = std::make_unique<Layer>(LayerType::CurrentRun);
+}
+
 static const std::map<System, std::string> system_to_name = {
     {System::Main, "Dolphin"},          {System::GCPad, "GCPad"},  {System::WiiPad, "Wiimote"},
     {System::GCKeyboard, "GCKeyboard"}, {System::GFX, "Graphics"}, {System::Logger, "Logger"},
diff --git a/Source/Core/Common/Config/Config.h b/Source/Core/Common/Config/Config.h
index ac5b1b5e4d..3ce1833345 100644
--- a/Source/Core/Common/Config/Config.h
+++ b/Source/Core/Common/Config/Config.h
@@ -40,6 +40,7 @@ void Save();
 
 void Init();
 void Shutdown();
+void ClearCurrentRunLayer();
 
 const std::string& GetSystemName(System system);
 System GetSystemFromName(const std::string& system);
diff --git a/Source/Core/Core/BootManager.cpp b/Source/Core/Core/BootManager.cpp
index 21dfe22ffa..e8fe2bd2c2 100644
--- a/Source/Core/Core/BootManager.cpp
+++ b/Source/Core/Core/BootManager.cpp
@@ -421,6 +421,7 @@ void Stop()
 
 void RestoreConfig()
 {
+  Config::ClearCurrentRunLayer();
   Config::RemoveLayer(Config::LayerType::Movie);
   Config::RemoveLayer(Config::LayerType::Netplay);
   Config::RemoveLayer(Config::LayerType::GlobalGame);