diff --git a/Mikado/subprograms/configure.py b/Mikado/subprograms/configure.py
index 988185fba..4509171e0 100644
--- a/Mikado/subprograms/configure.py
+++ b/Mikado/subprograms/configure.py
@@ -21,6 +21,7 @@
 import tempfile
 from ..utilities.log_utils import create_null_logger, create_default_logger
 import tomlkit
+import toml
 try:
     from yaml import CSafeLoader as yLoader
 except ImportError:
@@ -174,8 +175,10 @@ def create_config(args):
     if args.external is not None:
         if args.external.endswith("json"):
             loader = json.load
-        else:
+        elif args.external.endswith("yaml"):
             loader = functools.partial(yaml.load, Loader=yLoader)
+        else:
+            loader = toml.load
         with open(args.external) as external:
             external_conf = loader(external)
         # Overwrite values specific to Mikado