diff --git a/lib/galaxy/queue_worker/__init__.py b/lib/galaxy/queue_worker/__init__.py
index a998c012f00..74ef479a7da 100644
--- a/lib/galaxy/queue_worker/__init__.py
+++ b/lib/galaxy/queue_worker/__init__.py
@@ -296,6 +296,7 @@ def _get_new_toolbox(app: "UniverseApplication", save_integrated_tool_panel: boo
     tool_configs = app.config.tool_configs
 
     with app._toolbox_lock:
+        old_toolbox = app._toolbox
         new_toolbox: ToolBox
         if getattr(app.config, "use_lazy_toolbox", False) and getattr(app, "tool_source_store", None) is not None:
             new_toolbox = LazyToolBox(
@@ -320,6 +321,15 @@ def _get_new_toolbox(app: "UniverseApplication", save_integrated_tool_panel: boo
         for tool in new_toolbox.data_manager_tools.values():
             new_toolbox.register_tool(tool)
         app._toolbox = new_toolbox
+        # Retire the superseded box's background store watcher. In lazy mode
+        # each toolbox spawns a ToolSourceStoreWatcher daemon bound to itself;
+        # without this every reload leaks a polling thread that keeps grabbing
+        # app._toolbox_lock and disposing the shared store's engines on each
+        # republish. Only the watcher is stopped — in-flight reads on other
+        # threads still work, and the shared app.tool_source_store stays open.
+        # Eager ToolBoxes have no watcher, so guard on the lazy type.
+        if isinstance(old_toolbox, LazyToolBox) and old_toolbox is not new_toolbox:
+            old_toolbox.stop_watcher()
 
 
 def reload_data_managers(app, **kwargs):
diff --git a/lib/galaxy/tools/lazy_toolbox.py b/lib/galaxy/tools/lazy_toolbox.py
index 437669c37d1..9e5b073c8d8 100644
--- a/lib/galaxy/tools/lazy_toolbox.py
+++ b/lib/galaxy/tools/lazy_toolbox.py
@@ -1699,6 +1699,18 @@ class LazyToolBox(ToolBox):
             if entry and entry.hidden:
                 tool.hidden = True
 
+    def stop_watcher(self) -> None:
+        """Stop the background store-freshness watcher, if one is running.
+
+        The reload path uses this to retire a superseded toolbox's watcher
+        thread without the class-level ``ToolLineage.reset()`` and index/store
+        teardown of ``close()`` — the replacement box is already live and the
+        shared ``tool_source_store`` must stay open. Idempotent.
+        """
+        if self._store_watcher is not None:
+            self._store_watcher.shutdown()
+            self._store_watcher = None
+
     def close(self) -> None:
         """Drop in-memory state at app shutdown.
 
@@ -1708,9 +1720,7 @@ class LazyToolBox(ToolBox):
         ``tool_source_store`` before the next boot wires up a fresh
         toolbox. Idempotent; safe to call more than once.
         """
-        if self._store_watcher is not None:
-            self._store_watcher.shutdown()
-            self._store_watcher = None
+        self.stop_watcher()
         with self._cache_lock:
             self._tool_object_cache.clear()
         self._tool_index = None
diff --git a/test/unit/app/queue_worker/test_reload_toolbox_watcher.py b/test/unit/app/queue_worker/test_reload_toolbox_watcher.py
new file mode 100644
index 00000000000..0c87558f704
--- /dev/null
+++ b/test/unit/app/queue_worker/test_reload_toolbox_watcher.py
@@ -0,0 +1,68 @@
+import threading
+from types import SimpleNamespace
+from unittest.mock import MagicMock
+
+from galaxy import queue_worker
+from galaxy.queue_worker import _get_new_toolbox
+from galaxy.tools.lazy_toolbox import LazyToolBox
+
+
+class FakeWatcher:
+    def __init__(self):
+        self.stopped = False
+
+    def shutdown(self):
+        self.stopped = True
+
+
+def _fake_new_toolbox(*args, **kwargs):
+    box = SimpleNamespace(data_manager_tools={})
+    box.register_tool = lambda tool: None
+    return box
+
+
+def _fake_app(old_toolbox):
+    app = SimpleNamespace()
+    app._toolbox_lock = threading.RLock()
+    app._toolbox = old_toolbox
+    app.toolbox = old_toolbox
+    app.datatypes_registry = MagicMock()
+    app.tool_source_store = None
+    app.config = SimpleNamespace(
+        use_lazy_toolbox=False,
+        tool_configs=[],
+        tool_path="/tmp/tools",
+        lazy_toolbox_cache_size=500,
+    )
+    return app
+
+
+def _patch_builders(monkeypatch):
+    monkeypatch.setattr(queue_worker, "ToolBox", _fake_new_toolbox)
+    monkeypatch.setattr(queue_worker, "load_lib_tools", lambda toolbox: None)
+
+
+def test_replacement_stops_superseded_lazy_watcher(monkeypatch):
+    _patch_builders(monkeypatch)
+    old = LazyToolBox.__new__(LazyToolBox)
+    old.data_manager_tools = {}
+    watcher = FakeWatcher()
+    old._store_watcher = watcher  # type: ignore[assignment]
+    app = _fake_app(old)
+
+    _get_new_toolbox(app)
+
+    assert watcher.stopped is True
+    assert old._store_watcher is None
+    assert app._toolbox is not old
+
+
+def test_eager_old_toolbox_is_left_untouched(monkeypatch):
+    _patch_builders(monkeypatch)
+    old = SimpleNamespace(data_manager_tools={})
+    app = _fake_app(old)
+
+    _get_new_toolbox(app)
+
+    assert app._toolbox is not old
+    assert not hasattr(old, "_store_watcher")