diff --git a/pynxtools/nexus/nexus.py b/pynxtools/nexus/nexus.py
index 7da178b72..5af0cbf58 100644
--- a/pynxtools/nexus/nexus.py
+++ b/pynxtools/nexus/nexus.py
@@ -776,6 +776,10 @@ def process_nexus_master_file(self, parser):
 )
 def main(nexus_file, documentation, concept):
     """The main function to call when used as a script."""
+    import platform
+
+    if platform.system() == "Windows" and "Git" in os.environ["SHELL"]:
+        os.environ["MSYS_NO_PATHCONV"] = "1"
     logging_format = "%(levelname)s: %(message)s"
     stdout_handler = logging.StreamHandler(sys.stdout)
     stdout_handler.setLevel(logging.DEBUG)