diff --git a/addons/mod_loader/api/deprecated.gd b/addons/mod_loader/api/deprecated.gd
index d2cfca31..1ca5313f 100644
--- a/addons/mod_loader/api/deprecated.gd
+++ b/addons/mod_loader/api/deprecated.gd
@@ -61,7 +61,7 @@ static func deprecated_message(msg: String, since_version: String = "") -> void:
 #
 # Returns: void
 static func _deprecated_log(msg: String) -> void:
-	if ModLoaderStore.ml_options.ignore_deprecated_errors or OS.has_feature("standalone"):
+	if ModLoaderStore and ModLoaderStore.ml_options.ignore_deprecated_errors or OS.has_feature("standalone"):
 		ModLoaderLog.warning(msg, LOG_NAME)
 	else:
 		ModLoaderLog.fatal(msg, LOG_NAME)
diff --git a/addons/mod_loader/mod_loader.gd b/addons/mod_loader/mod_loader.gd
index e12b7117..7cc03df0 100644
--- a/addons/mod_loader/mod_loader.gd
+++ b/addons/mod_loader/mod_loader.gd
@@ -83,6 +83,7 @@ func _exit_tree() -> void:
 
 
 func _load_mods() -> void:
+	ModLoaderStore.previous_mod_dirs = _ModLoaderPath.get_dir_paths_in_dir(_ModLoaderPath.get_unpacked_mods_dir_path())
 	# Loop over "res://mods" and add any mod zips to the unpacked virtual
 	# directory (UNPACKED_DIR)
 	var zip_data := _load_mod_zips()
@@ -225,18 +226,17 @@ func _check_autoload_positions() -> void:
 		var _pos_ml_core := _ModLoaderGodot.check_autoload_position("ModLoader", 1, true)
 
 
-# Loop over "res://mods" and add any mod zips to the unpacked virtual directory
-# (UNPACKED_DIR)
+# Add any mod zips to the unpacked virtual directory
 func _load_mod_zips() -> Dictionary:
 	var zip_data := {}
 
-	if not ModLoaderStore.ml_options.steam_workshop_enabled:
+	if ModLoaderStore.ml_options.load_from_local:
 		var mods_folder_path := _ModLoaderPath.get_path_to_mods()
-
-		# If we're not using Steam workshop, just loop over the mod ZIPs.
+		# Loop over the mod zips in the "mods" directory
 		var loaded_zip_data := _ModLoaderFile.load_zips_in_folder(mods_folder_path)
 		zip_data.merge(loaded_zip_data)
-	else:
+	
+	if ModLoaderStore.ml_options.load_from_steam_workshop or ModLoaderStore.ml_options.steam_workshop_enabled:
 		# If we're using Steam workshop, loop over the workshop item directories
 		var loaded_workshop_zip_data := _ModLoaderSteam.load_steam_workshop_zips()
 		zip_data.merge(loaded_workshop_zip_data)
@@ -254,7 +254,7 @@ func _setup_mods() -> int:
 	if dir == null:
 		ModLoaderLog.error("Can't open unpacked mods folder %s." % unpacked_mods_path, LOG_NAME)
 		return -1
-	if not dir.list_dir_begin() == OK:# TODOGODOT4 fill missing arguments https://github.com/godotengine/godot/pull/40547
+	if not dir.list_dir_begin() == OK:
 		ModLoaderLog.error("Can't read unpacked mods folder %s." % unpacked_mods_path, LOG_NAME)
 		return -1
 
diff --git a/addons/mod_loader/mod_loader_store.gd b/addons/mod_loader/mod_loader_store.gd
index 54775ec2..bf9622e2 100644
--- a/addons/mod_loader/mod_loader_store.gd
+++ b/addons/mod_loader/mod_loader_store.gd
@@ -111,6 +111,7 @@ var ml_options := {
 
 	# If true, ModLoader will load mod ZIPs from the Steam workshop directory,
 	# instead of the default location (res://mods)
+	# INFO: Redundant since the introduction of mod source options, kept for backwards compatibility.
 	steam_workshop_enabled = false,
 
 	# Overrides for the path mods/configs/workshop folders are loaded from.
@@ -130,6 +131,12 @@ var ml_options := {
 
 	# Array of mods that should be ignored when logging messages (contains mod IDs as strings)
 	ignored_mod_names_in_log = [],
+
+	# Mod Sources
+	# Indicates whether to load mods from the Steam Workshop directory, or the overridden workshop path.
+	load_from_steam_workshop = false,
+	# Indicates whether to load mods from the "mods" folder located at the game's install directory, or the overridden mods path.
+	load_from_local = true,
 }
 
 
@@ -169,6 +176,8 @@ func _update_ml_options_from_options_resource() -> void:
 		# Update from the options in the resource
 		for key in ml_options:
 			ml_options[key] = current_options[key]
+			if key == "steam_workshop_enabled" and current_options[key] == true:
+				ModLoaderDeprecated.deprecated_message("The Steam Workshop Enabled option has been deprecated. Please use the mod source options instead.", "6.3.0")
 
 	# Get options overrides by feature tags
 	# An override is saved as Dictionary[String: ModLoaderOptionsProfile]
@@ -199,6 +208,8 @@ func _update_ml_options_from_options_resource() -> void:
 		# Update from the options in the resource
 		for key in ml_options:
 			ml_options[key] = override_options[key]
+			if key == "steam_workshop_enabled" and override_options[key] == true:
+				ModLoaderDeprecated.deprecated_message("The Steam Workshop Enabled option has been deprecated. Please use the mod source options instead.", "6.3.0")
 
 
 # Update ModLoader's options, via CLI args
diff --git a/addons/mod_loader/resources/options_profile.gd b/addons/mod_loader/resources/options_profile.gd
index 0f54dbbf..619e9080 100644
--- a/addons/mod_loader/resources/options_profile.gd
+++ b/addons/mod_loader/resources/options_profile.gd
@@ -16,3 +16,8 @@ extends Resource
 @export_dir var override_path_to_workshop = ""
 @export var ignore_deprecated_errors: bool = false
 @export var ignored_mod_names_in_log: Array[String] = []
+@export_group("Mod Source")
+## Indicates whether to load mods from the Steam Workshop directory, or the overridden workshop path.
+@export var load_from_steam_workshop: bool = false
+## Indicates whether to load mods from the "mods" folder located at the game's install directory, or the overridden mods path.
+@export var load_from_local: bool = true