diff --git a/python/sdist/amici/__init__.py b/python/sdist/amici/__init__.py
index d51dcdb72c..2e29bc17f7 100644
--- a/python/sdist/amici/__init__.py
+++ b/python/sdist/amici/__init__.py
@@ -197,6 +197,14 @@ def import_model_module(
             module_name,
             f"_{module_name}{ext_suffix}",
         )
+        if not needed_file.exists():
+            # if we import a matlab-generated model where the extension
+            #  is in a different directory
+            needed_file = Path(
+                module_path,
+                f"_{module_name}{ext_suffix}",
+            )
+
         if not loaded_file.samefile(needed_file):
             # this is not the right module, and we can't unload it
             raise RuntimeError(