diff --git a/planemo/autoupdate.py b/planemo/autoupdate.py
index 289738ac1..34ea33667 100644
--- a/planemo/autoupdate.py
+++ b/planemo/autoupdate.py
@@ -28,6 +28,7 @@
 from planemo.io import (
     error,
     info,
+    warn,
 )
 from planemo.workflow_lint import (
     find_repos_from_tool_id,
@@ -78,6 +79,18 @@ def get_tokens(xml_tree: ElementTree) -> Dict[str, Dict[str, Optional[str]]]:
     return tokens
 
 
+def parse_version(version: str) -> packaging.version.Version:
+    """
+    Parse a version string into a Version object.
+    If the version string is not PEP 440 compliant, return Version("0").
+    """
+    try:
+        return packaging.version.parse(version)
+    except packaging.version.InvalidVersion as e:
+        warn(e)
+        return packaging.version.Version("0")
+
+
 def check_conda(package_name: str, ctx: "PlanemoCliContext", **kwds) -> str:
     """
     Get the most up-to-date conda version for a package.
@@ -89,7 +102,7 @@ def check_conda(package_name: str, ctx: "PlanemoCliContext", **kwds) -> str:
         search_results = itertools.chain.from_iterable(
             n["versions"] for n in r.json() if n["name"] == package_name and n["owner"] in kwds["conda_ensure_channels"]
         )
-        return sorted(search_results, key=packaging.version.parse, reverse=True)[0]
+        return sorted(search_results, key=parse_version, reverse=True)[0]
 
     target = conda_util.CondaTarget(package_name)
     best_search_results = conda_util.best_search_result(target, conda_context=conda_context)
@@ -289,7 +302,7 @@ def _update_wf(config: "LocalGalaxyConfig", workflow_id: str, instance: bool = F
 def get_newest_tool_id(tool_ids: List[str]) -> str:
     return sorted(
         tool_ids,
-        key=lambda n: packaging.version.parse(n.split("/")[-1]),
+        key=lambda n: parse_version(n.split("/")[-1]),
     )[-1]