diff --git a/homeassistant/bootstrap.py b/homeassistant/bootstrap.py
index 66312f7283a..3877a6bf6e1 100644
--- a/homeassistant/bootstrap.py
+++ b/homeassistant/bootstrap.py
@@ -564,6 +564,14 @@ async def _async_set_up_integrations(
         except asyncio.TimeoutError:
             _LOGGER.warning("Setup timed out for stage 2 - moving forward")
 
+    # Wrap up startup
+    _LOGGER.debug("Waiting for startup to wrap up")
+    try:
+        async with hass.timeout.async_timeout(WRAP_UP_TIMEOUT, cool_down=COOLDOWN_TIME):
+            await hass.async_block_till_done()
+    except asyncio.TimeoutError:
+        _LOGGER.warning("Setup timed out for bootstrap - moving forward")
+
     watch_task.cancel()
     async_dispatcher_send(hass, SIGNAL_BOOTSTRAP_INTEGRATONS, {})
 
@@ -576,11 +584,3 @@ async def _async_set_up_integrations(
             )
         },
     )
-
-    # Wrap up startup
-    _LOGGER.debug("Waiting for startup to wrap up")
-    try:
-        async with hass.timeout.async_timeout(WRAP_UP_TIMEOUT, cool_down=COOLDOWN_TIME):
-            await hass.async_block_till_done()
-    except asyncio.TimeoutError:
-        _LOGGER.warning("Setup timed out for bootstrap - moving forward")
diff --git a/tests/test_bootstrap.py b/tests/test_bootstrap.py
index 3eeb06d056c..1ad64e58bd7 100644
--- a/tests/test_bootstrap.py
+++ b/tests/test_bootstrap.py
@@ -678,6 +678,7 @@ async def test_empty_integrations_list_is_only_sent_at_the_end_of_bootstrap(hass
         await bootstrap._async_set_up_integrations(
             hass, {"normal_integration": {}, "an_after_dep": {}}
         )
+        await hass.async_block_till_done()
 
     assert integrations[0] != {}
     assert "an_after_dep" in integrations[0]
@@ -686,3 +687,35 @@ async def test_empty_integrations_list_is_only_sent_at_the_end_of_bootstrap(hass
 
     assert "normal_integration" in hass.config.components
     assert order == ["an_after_dep", "normal_integration"]
+
+
+@pytest.mark.parametrize("load_registries", [False])
+async def test_warning_logged_on_wrap_up_timeout(hass, caplog):
+    """Test we log a warning on bootstrap timeout."""
+
+    def gen_domain_setup(domain):
+        async def async_setup(hass, config):
+            await asyncio.sleep(0.1)
+
+            async def _background_task():
+                await asyncio.sleep(0.2)
+
+            await hass.async_create_task(_background_task())
+            return True
+
+        return async_setup
+
+    mock_integration(
+        hass,
+        MockModule(
+            domain="normal_integration",
+            async_setup=gen_domain_setup("normal_integration"),
+            partial_manifest={},
+        ),
+    )
+
+    with patch.object(bootstrap, "WRAP_UP_TIMEOUT", 0):
+        await bootstrap._async_set_up_integrations(hass, {"normal_integration": {}})
+        await hass.async_block_till_done()
+
+    assert "Setup timed out for bootstrap - moving forward" in caplog.text