diff --git a/lib/galaxy/queue_worker/__init__.py b/lib/galaxy/queue_worker/__init__.py
index e71ca5f7c03..a998c012f00 100644
--- a/lib/galaxy/queue_worker/__init__.py
+++ b/lib/galaxy/queue_worker/__init__.py
@@ -286,33 +286,40 @@ def _get_new_toolbox(app: "UniverseApplication", save_integrated_tool_panel: boo
     """
     Generate a new toolbox, by constructing a toolbox from the config files,
     and then adding pre-existing data managers from the old toolbox to the new toolbox.
+
+    Serialized under ``app._toolbox_lock`` against ``remove_tool_by_id`` and
+    ``invalidate_index_cache``: a reload queued by an earlier conf write (the
+    install that precedes an uninstall) otherwise interleaves its rebuild —
+    including a potentially long inline index populate — with the removal,
+    and the swapped-in toolbox resurrects the just-removed tool.
     """
     tool_configs = app.config.tool_configs
 
-    new_toolbox: ToolBox
-    if getattr(app.config, "use_lazy_toolbox", False) and getattr(app, "tool_source_store", None) is not None:
-        new_toolbox = LazyToolBox(
-            config_filenames=tool_configs,
-            tool_root_dir=app.config.tool_path,
-            app=app,
-            tool_source_store=app.tool_source_store,
-            cache_size=getattr(app.config, "lazy_toolbox_cache_size", 500),
-            save_integrated_tool_panel=save_integrated_tool_panel,
-        )
-    else:
-        new_toolbox = ToolBox(
-            tool_configs,
-            app.config.tool_path,
-            app,
-            save_integrated_tool_panel=save_integrated_tool_panel,
-        )
-    new_toolbox.data_manager_tools = app.toolbox.data_manager_tools
-    app.datatypes_registry.load_datatype_converters(new_toolbox, use_cached=True)
-    app.datatypes_registry.load_external_metadata_tool(new_toolbox)
-    load_lib_tools(new_toolbox)
-    for tool in new_toolbox.data_manager_tools.values():
-        new_toolbox.register_tool(tool)
-    app._toolbox = new_toolbox
+    with app._toolbox_lock:
+        new_toolbox: ToolBox
+        if getattr(app.config, "use_lazy_toolbox", False) and getattr(app, "tool_source_store", None) is not None:
+            new_toolbox = LazyToolBox(
+                config_filenames=tool_configs,
+                tool_root_dir=app.config.tool_path,
+                app=app,
+                tool_source_store=app.tool_source_store,
+                cache_size=getattr(app.config, "lazy_toolbox_cache_size", 500),
+                save_integrated_tool_panel=save_integrated_tool_panel,
+            )
+        else:
+            new_toolbox = ToolBox(
+                tool_configs,
+                app.config.tool_path,
+                app,
+                save_integrated_tool_panel=save_integrated_tool_panel,
+            )
+        new_toolbox.data_manager_tools = app.toolbox.data_manager_tools
+        app.datatypes_registry.load_datatype_converters(new_toolbox, use_cached=True)
+        app.datatypes_registry.load_external_metadata_tool(new_toolbox)
+        load_lib_tools(new_toolbox)
+        for tool in new_toolbox.data_manager_tools.values():
+            new_toolbox.register_tool(tool)
+        app._toolbox = new_toolbox
 
 
 def reload_data_managers(app, **kwargs):
diff --git a/lib/galaxy/tools/lazy_toolbox.py b/lib/galaxy/tools/lazy_toolbox.py
index 0d47da823f0..437669c37d1 100644
--- a/lib/galaxy/tools/lazy_toolbox.py
+++ b/lib/galaxy/tools/lazy_toolbox.py
@@ -1774,6 +1774,16 @@ class LazyToolBox(ToolBox):
                     send_control_task(self.app, "reload_tool_source_cache", noop_self=True)
                 except Exception as e:
                     log.warning("Broadcasting index removal of %s raised: %s", tool_id, e)
+            # A toolbox reload queued before this removal (the conf write of
+            # the preceding install) may already have swapped a NEW toolbox
+            # into ``app.toolbox``, built from the index as it stood before
+            # ``remove_index_entry`` above — with the tool still registered.
+            # ``self`` is then the superseded instance and cleaning it alone
+            # leaves ``app.toolbox`` serving the uninstalled tool. The swap
+            # holds the same lock, so the current object is stable here.
+            current = getattr(self.app, "toolbox", None)
+            if current is not self and isinstance(current, LazyToolBox):
+                current._remove_tool_in_memory(tool_id, remove_from_panel=remove_from_panel)
         return result
 
     def _remove_tool_in_memory(self, tool_id: str, remove_from_panel: bool = True):
diff --git a/test/unit/app/tools/test_lazy_tool.py b/test/unit/app/tools/test_lazy_tool.py
index e0fbce9cb9d..e6114d7fba2 100644
--- a/test/unit/app/tools/test_lazy_tool.py
+++ b/test/unit/app/tools/test_lazy_tool.py
@@ -564,6 +564,25 @@ def test_remove_tool_by_id_broadcasts_reload_to_peers(monkeypatch):
     assert "doomed" not in box._tools_by_id
 
 
+def test_remove_tool_by_id_also_cleans_swapped_in_toolbox(monkeypatch):
+    # A reload queued before the removal can swap a new toolbox into
+    # app.toolbox, rebuilt from the pre-removal index — cleaning only
+    # ``self`` would leave the new box serving the uninstalled tool.
+    old_box = _registry_box()
+    new_box = _registry_box()
+    entry = _entry(id="doomed")
+    for box in (old_box, new_box):
+        box._tool_index = ToolIndex()
+        box._tool_index.add_entry(entry)
+        box._register_lazy_entry(entry)
+    old_box.app.toolbox = new_box
+    monkeypatch.setattr(queue_worker_mod, "send_control_task", lambda app, task, **kwargs: None)
+    old_box.remove_tool_by_id("doomed")
+    assert "doomed" not in old_box._tools_by_id
+    assert "doomed" not in new_box._tools_by_id
+    assert "tool_doomed" not in new_box._tool_panel
+
+
 def test_tool_file_on_disk_answers_from_index(tmp_path):
     box = _seam_box()
     box._index_source_paths_cache = None