diff --git a/src/simdb/cli/manifest.py b/src/simdb/cli/manifest.py
index 77ba7d05..739bf32e 100644
--- a/src/simdb/cli/manifest.py
+++ b/src/simdb/cli/manifest.py
@@ -1,6 +1,7 @@
 import os
 import re
 import urllib.parse
+import warnings
 from enum import Enum, auto
 from pathlib import Path
 from typing import Dict, Iterable, List, Optional, TextIO, Tuple, Type, Union
@@ -564,7 +565,18 @@ def validate(self) -> None:
             )
 
         if "manifest_version" not in self._data:
-            print("warning: no version given in manifest, assuming version 2.")
+            if "version" in self._data and self._data["version"] == 1:
+                warnings.warn(
+                    "Found version field for manifest version 1, please update "
+                    "to manifest_version",
+                    DeprecationWarning,
+                    stacklevel=1,
+                )
+                self._data["manifest_version"] = self._data.pop("version")
+            else:
+                warnings.warn(
+                    "No version given in manifest, assuming version 2.", stacklevel=1
+                )
 
         version = self.version