diff --git a/janus_core/training/preprocess.py b/janus_core/training/preprocess.py
index 11b3b08b..dcfc0be0 100644
--- a/janus_core/training/preprocess.py
+++ b/janus_core/training/preprocess.py
@@ -64,8 +64,17 @@ def preprocess(
     if logger and "foundation_model" in options:
         logger.info("Fine tuning model: %s", options["foundation_model"])
 
-    # Path must be passed as a string
-    mlip_args = mace_parser().parse_args(["--config", str(mlip_config)])
+    # Parse options from config, as MACE cannot read config file yet
+    args = []
+    for key, value in options.items():
+        if isinstance(value, bool):
+            if value is True:
+                args.append(f"--{key}")
+        else:
+            args.append(f"--{key}")
+            args.append(f"{value}")
+
+    mlip_args = mace_parser().parse_args(args)
 
     if logger:
         logger.info("Starting preprocessing")