diff --git a/lib/galaxy/tool_source_store/database.py b/lib/galaxy/tool_source_store/database.py
index 4e42be66398..ebc9816440a 100644
--- a/lib/galaxy/tool_source_store/database.py
+++ b/lib/galaxy/tool_source_store/database.py
@@ -310,7 +310,11 @@ class DatabaseToolSourceStore(ToolSourceStore):
         if index is None:
             index = ToolIndex()
 
-        index.entries[entry.id] = entry
+        # add_entry keeps ``entries_by_version`` in step with ``entries`` —
+        # versioned lookups (``get(tool_id, tool_version)``, the job-time
+        # materialise path) read the per-version map, and the two maps are
+        # serialized independently.
+        index.add_entry(entry)
         index.invalidate_caches()
 
         # Update section mapping
diff --git a/lib/galaxy/tools/lazy_toolbox.py b/lib/galaxy/tools/lazy_toolbox.py
index e1d9ad75d27..9a868534956 100644
--- a/lib/galaxy/tools/lazy_toolbox.py
+++ b/lib/galaxy/tools/lazy_toolbox.py
@@ -801,6 +801,13 @@ class LazyToolBox(ToolBox):
             # id and misses the registry. Persist so job-handler processes
             # materialising from the shared index see it too.
             entry.data_manager_id = data_manager_id
+            if self._tool_index is not None:
+                # After a from_dict reload the default and per-version maps
+                # hold distinct objects; the job-time materialise resolves
+                # through the per-version map, so stamp its twin too.
+                twin = self._tool_index.entries_by_version.get(entry.id, {}).get(entry.version or "")
+                if twin is not None and twin is not entry:
+                    twin.data_manager_id = data_manager_id
             if self._store is not None:
                 try:
                     self._store.update_index_entry(entry)
diff --git a/test/unit/app/tools/test_lazy_tool.py b/test/unit/app/tools/test_lazy_tool.py
index 289ef621b52..538e7b4d805 100644
--- a/test/unit/app/tools/test_lazy_tool.py
+++ b/test/unit/app/tools/test_lazy_tool.py
@@ -360,9 +360,14 @@ def test_create_tool_stamps_data_manager_conf_id_on_entry():
     box = _seam_box()
     e = _entry(id="dm_tool", tool_type="manage_data")
     box._tool_index.entries["dm_tool"] = e
+    # After a from_dict reload the per-version map holds a distinct object —
+    # the one job-time versioned lookups resolve. It must get the stamp too.
+    twin = _entry(id="dm_tool", tool_type="manage_data")
+    box._tool_index.entries_by_version["dm_tool"] = {twin.version or "": twin}
     tool = box.create_tool(config_file=None, guid="dm_tool", data_manager_id="test_data_manager")
     assert isinstance(tool, LazyTool)
     assert e.data_manager_id == "test_data_manager"
+    assert twin.data_manager_id == "test_data_manager"
     box._store.update_index_entry.assert_called_once_with(e)
 
 
diff --git a/test/unit/tool_source_store/test_stores.py b/test/unit/tool_source_store/test_stores.py
index 8f062cd0fc5..5136323a578 100644
--- a/test/unit/tool_source_store/test_stores.py
+++ b/test/unit/tool_source_store/test_stores.py
@@ -213,6 +213,24 @@ class TestDatabaseBackendPathRows:
         assert reloaded.get("removable") is None
         assert "removable" not in reloaded.by_section.get("sec1", [])
 
+    def test_update_index_entry_reaches_versioned_lookups(self):
+        app = MockApp()
+        store = DatabaseToolSourceStore(app.model.context)  # type: ignore[arg-type]
+        index = ToolIndex()
+        index.add_entry(ToolIndexEntry(id="dm_tool", version="1.0", name="DM"))
+        store.store_index(index)
+        app.model.context.commit()
+
+        store.update_index_entry(ToolIndexEntry(id="dm_tool", version="1.0", name="DM", data_manager_id="conf_id"))
+        app.model.context.commit()
+        store.invalidate_index_cache()
+
+        reloaded = store.load_index()
+        assert reloaded is not None
+        versioned = reloaded.get("dm_tool", "1.0")
+        assert versioned is not None
+        assert versioned.data_manager_id == "conf_id"
+
     def test_pathless_sources_dedupe_on_hash(self):
         app = MockApp()
         store = DatabaseToolSourceStore(app.model.context)  # type: ignore[arg-type]