diff --git a/lib/galaxy/tool_util/toolbox/base.py b/lib/galaxy/tool_util/toolbox/base.py
index 4529f85d40db..4742e7b7c32f 100644
--- a/lib/galaxy/tool_util/toolbox/base.py
+++ b/lib/galaxy/tool_util/toolbox/base.py
@@ -96,7 +96,12 @@ def __init__(self, toolbox: "AbstractToolBox"):
 
     def has_tool(self, tool_id: str) -> bool:
         toolbox = self.__toolbox
-        return tool_id in toolbox._tools_by_id or tool_id in toolbox._tools_by_old_id
+        # tool_id could be full guid, old tool id (no toolshed and version info) or versionless guid.
+        return (
+            tool_id in toolbox._tools_by_id
+            or tool_id in toolbox._tools_by_old_id
+            or bool(toolbox._lineage_map.lineage_map.get(tool_id))
+        )
 
     def get_tool(self, tool_id: str):
         return self.__toolbox.get_tool(tool_id)
diff --git a/lib/galaxy/tool_util/toolbox/lineages/factory.py b/lib/galaxy/tool_util/toolbox/lineages/factory.py
index 96efb51d77d1..2a68c32b2ee4 100644
--- a/lib/galaxy/tool_util/toolbox/lineages/factory.py
+++ b/lib/galaxy/tool_util/toolbox/lineages/factory.py
@@ -44,7 +44,15 @@ def get(self, tool_id) -> Optional[ToolLineage]:
         if lineage:
             return lineage
         if tool_id not in self.lineage_map:
-            tool = self.app.toolbox._tools_by_id.get(tool_id)
+            toolbox = None
+            try:
+                toolbox = self.app.toolbox
+            except AttributeError:
+                # We're building the lineage map while building the toolbox,
+                # so app.toolbox may not be available.
+                # TODO: is the fallback really needed / can it be fixed by improving _get_versionless ?
+                pass
+            tool = toolbox and toolbox._tools_by_id.get(tool_id)
             if tool:
                 lineage = ToolLineage.from_tool(tool)
             if lineage: