diff --git a/rmgpy/rmg/main.py b/rmgpy/rmg/main.py
index 01763b7605..9d1b266ddf 100644
--- a/rmgpy/rmg/main.py
+++ b/rmgpy/rmg/main.py
@@ -1342,6 +1342,10 @@ def make_seed_mech(self):
         temp_seed_dir = os.path.join(self.output_directory, 'seed_tmp')
 
         # Move the seed from the previous iteration to a temporary directory in case we run into errors
+
+        # First, remove the temporary seed mechanism if it exists from a previous run
+        if os.path.exists(temp_seed_dir):
+            shutil.rmtree(temp_seed_dir)
         try:
             os.rename(seed_dir, temp_seed_dir)
         except PermissionError:  # The Windows Subsystem for Linux (WSL) can have problems with renaming