diff --git a/src/osdep/amiberry_whdbooter.cpp b/src/osdep/amiberry_whdbooter.cpp
index 2cc16ee0d..e3f02e80a 100644
--- a/src/osdep/amiberry_whdbooter.cpp
+++ b/src/osdep/amiberry_whdbooter.cpp
@@ -1189,6 +1189,7 @@ void set_booter_drives(uae_prefs* prefs, const char* filepath)
 
 void whdload_auto_prefs(uae_prefs* prefs, const char* filepath)
 {
+	bool custom_config_loaded = false;
 	write_log("WHDBooter Launched\n");
 
 	if (lstAvailableROMs.empty())
@@ -1216,18 +1217,7 @@ void whdload_auto_prefs(uae_prefs* prefs, const char* filepath)
 	const std::string filename_no_extension = get_game_filename(filepath);
 	whdload_prefs.filename = filename_no_extension;
 
-	// LOAD GAME SPECIFICS FOR EXISTING .UAE - USE SHA1 IF AVAILABLE
-	//  CONFIG LOAD IF .UAE IS IN CONFIG PATH
-	build_uae_config_filename(whdload_prefs.filename);
-
-	// If we have a config file, we use that first
-	if (std::filesystem::exists(uae_config))
-	{
-		write_log("WHDBooter -  %s found. Loading Config for WHDLoad options.\n", uae_config.c_str());
-		target_cfgfile_load(prefs, uae_config.c_str(), CONFIG_TYPE_DEFAULT, 0);
-	}
-
-	// setups for tmp folder.
+	// setup for tmp folder.
 	std::filesystem::create_directories("/tmp/amiberry/s");
 	std::filesystem::create_directories("/tmp/amiberry/c");
 	std::filesystem::create_directories("/tmp/amiberry/devs");
@@ -1243,7 +1233,6 @@ void whdload_auto_prefs(uae_prefs* prefs, const char* filepath)
 	// LOAD GAME SPECIFICS
 	whd_path = whdbooter_path / "game-data";
 	game_hardware_options game_detail;
-
 	whd_config = whd_path / "whdload_db.xml";
 
 	if (std::filesystem::exists(whd_config))
@@ -1252,7 +1241,17 @@ void whdload_auto_prefs(uae_prefs* prefs, const char* filepath)
 	}
 	else
 	{
-		write_log("WHDBooter -  Could not load whdload_db.xml - does not exist?\n");
+		write_log("WHDBooter - Could not load whdload_db.xml - does not exist?\n");
+	}
+
+	// LOAD CUSTOM CONFIG
+	build_uae_config_filename(whdload_prefs.filename);
+	// If we have a config file, we will load that on top of the XML settings
+	if (std::filesystem::exists(uae_config))
+	{
+		write_log("WHDBooter - %s found. Loading Config for WHDLoad options.\n", uae_config.c_str());
+		target_cfgfile_load(prefs, uae_config.c_str(), CONFIG_TYPE_DEFAULT, 0);
+		custom_config_loaded = true;
 	}
 
 	// If we have a slave, create a startup-sequence
@@ -1318,7 +1317,7 @@ void whdload_auto_prefs(uae_prefs* prefs, const char* filepath)
 #endif
 
 	// if we already loaded a .uae config, we don't need to do the below manual setup for hardware
-	if (std::filesystem::exists(uae_config))
+	if (custom_config_loaded)
 	{
 		write_log("WHDBooter - %s found; ignoring WHD Quickstart setup.\n", uae_config.c_str());
 		return;