diff --git a/chai_lab/chai1.py b/chai_lab/chai1.py
index c630618..4ac2031 100644
--- a/chai_lab/chai1.py
+++ b/chai_lab/chai1.py
@@ -7,6 +7,7 @@
 from collections import Counter
 from dataclasses import dataclass
 from pathlib import Path
+from tempfile import TemporaryDirectory
 
 import numpy as np
 import torch
@@ -313,12 +314,13 @@ def run_inference(
             for chain in chains
             if chain.entity_data.entity_type == EntityType.PROTEIN
         ]
-        msa_dir = output_dir / "mmseqs_msas"
-        msa_dir.mkdir(exist_ok=False, parents=True)
-        generate_colabfold_msas(protein_seqs=protein_sequences, msa_dir=msa_dir)
-        msa_context, msa_profile_context = get_msa_contexts(
-            chains, msa_directory=msa_dir
-        )
+        # Save MSAs to temporary directory to ensure we never clobber anything
+        with TemporaryDirectory() as tmpdir:
+            msa_dir = Path(tmpdir)
+            generate_colabfold_msas(protein_seqs=protein_sequences, msa_dir=msa_dir)
+            msa_context, msa_profile_context = get_msa_contexts(
+                chains, msa_directory=msa_dir
+            )
     elif msa_directory is not None:
         msa_context, msa_profile_context = get_msa_contexts(
             chains, msa_directory=msa_directory