diff --git a/pcsx2/Config.h b/pcsx2/Config.h
index 0832a08837..f2554bd534 100644
--- a/pcsx2/Config.h
+++ b/pcsx2/Config.h
@@ -1025,6 +1025,9 @@ struct Pcsx2Config
 	// You shouldn't assign to this class, because it'll mess with the runtime variables (Current...).
 	// But you can still use this to copy config. Only needed until we drop wx.
 	void CopyConfig(const Pcsx2Config& cfg);
+
+	/// Copies runtime configuration settings (e.g. frame limiter state).
+	void CopyRuntimeConfig(Pcsx2Config& cfg);
 };
 
 extern Pcsx2Config EmuConfig;
diff --git a/pcsx2/Pcsx2Config.cpp b/pcsx2/Pcsx2Config.cpp
index 2d4ab942fe..16e004e361 100644
--- a/pcsx2/Pcsx2Config.cpp
+++ b/pcsx2/Pcsx2Config.cpp
@@ -1238,6 +1238,17 @@ void Pcsx2Config::CopyConfig(const Pcsx2Config& cfg)
 	LimiterMode = cfg.LimiterMode;
 }
 
+void Pcsx2Config::CopyRuntimeConfig(Pcsx2Config& cfg)
+{
+	GS.LimitScalar = cfg.GS.LimitScalar;
+	UseBOOT2Injection = cfg.UseBOOT2Injection;
+	CurrentBlockdump = std::move(cfg.CurrentBlockdump);
+	CurrentIRX = std::move(cfg.CurrentIRX);
+	CurrentGameArgs = std::move(cfg.CurrentGameArgs);
+	CurrentAspectRatio = cfg.CurrentAspectRatio;
+	LimiterMode = cfg.LimiterMode;
+}
+
 void EmuFolders::SetDefaults(SettingsInterface& si)
 {
 	si.SetStringValue("Folders", "Bios", "bios");
diff --git a/pcsx2/VMManager.cpp b/pcsx2/VMManager.cpp
index 9f496ceba5..5f07846b20 100644
--- a/pcsx2/VMManager.cpp
+++ b/pcsx2/VMManager.cpp
@@ -1673,7 +1673,11 @@ void VMManager::ApplySettings()
 		GetMTGS().WaitGS(false);
 	}
 
-	const Pcsx2Config old_config(EmuConfig);
+	// Reset to a clean Pcsx2Config. Otherwise things which are optional (e.g. gamefixes)
+	// do not use the correct default values when loading.
+	Pcsx2Config old_config(std::move(EmuConfig));
+	EmuConfig = Pcsx2Config();
+	EmuConfig.CopyRuntimeConfig(old_config);
 	LoadSettings();
 	CheckForConfigChanges(old_config);
 }