diff --git a/homeassistant/core.py b/homeassistant/core.py
index 48702c15513530..5ec94f69045cb2 100644
--- a/homeassistant/core.py
+++ b/homeassistant/core.py
@@ -273,6 +273,7 @@ def async_stop(self) -> None:
         self.bus.async_fire(EVENT_HOMEASSISTANT_STOP)
         yield from self.loop.run_in_executor(None, self.pool.block_till_done)
         yield from self.loop.run_in_executor(None, self.pool.stop)
+        self.executer.shutdown()
         self.state = CoreState.not_running
         self.loop.stop()
 
diff --git a/tests/common.py b/tests/common.py
index e75de06013e893..ffc5d13b2be302 100644
--- a/tests/common.py
+++ b/tests/common.py
@@ -55,10 +55,17 @@ def get_test_home_assistant(num_threads=None):
         loader.prepare(hass)
 
     # FIXME should not be a daemon. Means hass.stop() not called in teardown
-    threading.Thread(name="LoopThread", target=loop.run_forever,
-                     daemon=True).start()
+    stop_event = threading.Event()
+
+    def run_loop():
+        loop.run_forever()
+        loop.close()
+        stop_event.set()
+
+    threading.Thread(name="LoopThread", target=run_loop, daemon=True).start()
 
     orig_start = hass.start
+    orig_stop = hass.stop
 
     @asyncio.coroutine
     def fake_stop():
@@ -72,7 +79,12 @@ def start_hass():
                     orig_start()
                     hass.block_till_done()
 
+    def stop_hass():
+        orig_stop()
+        stop_event.wait()
+
     hass.start = start_hass
+    hass.stop = stop_hass
 
     return hass
 
diff --git a/tests/test_bootstrap.py b/tests/test_bootstrap.py
index 8ad9d1cc409f11..b2a3136455a93a 100644
--- a/tests/test_bootstrap.py
+++ b/tests/test_bootstrap.py
@@ -29,6 +29,9 @@ def setup_method(self, method):
 
     def teardown_method(self, method):
         """Clean up."""
+        if method == self.test_from_config_file:
+            return
+
         dt_util.DEFAULT_TIME_ZONE = ORIG_TIMEZONE
         self.hass.stop()
         loader._COMPONENT_CACHE = self.backup_cache