diff --git a/homeassistant/bootstrap.py b/homeassistant/bootstrap.py
index 0676cec7fad..c764bfe8c21 100644
--- a/homeassistant/bootstrap.py
+++ b/homeassistant/bootstrap.py
@@ -115,11 +115,6 @@ async def async_from_config_dict(config: Dict[str, Any],
     conf_util.merge_packages_config(
         hass, config, core_config.get(conf_util.CONF_PACKAGES, {}))
 
-    # Ensure we have no None values after merge
-    for key, value in config.items():
-        if not value:
-            config[key] = {}
-
     hass.config_entries = config_entries.ConfigEntries(hass, config)
     await hass.config_entries.async_load()
 
diff --git a/homeassistant/config.py b/homeassistant/config.py
index 5f7107f95ae..4fc77bd81cd 100644
--- a/homeassistant/config.py
+++ b/homeassistant/config.py
@@ -332,7 +332,7 @@ async def async_hass_config_yaml(hass: HomeAssistant) -> Dict:
     """Load YAML from a Home Assistant configuration file.
 
     This function allow a component inside the asyncio loop to reload its
-    configuration by itself.
+    configuration by itself. Include package merge.
 
     This method is a coroutine.
     """
@@ -341,7 +341,10 @@ async def async_hass_config_yaml(hass: HomeAssistant) -> Dict:
         if path is None:
             raise HomeAssistantError(
                 "Config file not found in: {}".format(hass.config.config_dir))
-        return load_yaml_config_file(path)
+        config = load_yaml_config_file(path)
+        core_config = config.get(CONF_CORE, {})
+        merge_packages_config(hass, config, core_config.get(CONF_PACKAGES, {}))
+        return config
 
     return await hass.async_add_executor_job(_load_hass_yaml_config)
 
diff --git a/homeassistant/scripts/check_config.py b/homeassistant/scripts/check_config.py
index 1e77454a8d5..ac341e8f58a 100644
--- a/homeassistant/scripts/check_config.py
+++ b/homeassistant/scripts/check_config.py
@@ -327,11 +327,6 @@ def check_ha_config_file(hass):
         hass, config, core_config.get(CONF_PACKAGES, {}), _pack_error)
     core_config.pop(CONF_PACKAGES, None)
 
-    # Ensure we have no None values after merge
-    for key, value in config.items():
-        if not value:
-            config[key] = {}
-
     # Filter out repeating config sections
     components = set(key.split(' ')[0] for key in config.keys())
 
diff --git a/tests/test_config.py b/tests/test_config.py
index 0d248e2b170..212fc247eb9 100644
--- a/tests/test_config.py
+++ b/tests/test_config.py
@@ -6,8 +6,10 @@ import unittest
 import unittest.mock as mock
 from collections import OrderedDict
 
+import asynctest
 import pytest
 from voluptuous import MultipleInvalid, Invalid
+import yaml
 
 from homeassistant.core import DOMAIN, HomeAssistantError, Config
 import homeassistant.config as config_util
@@ -31,7 +33,8 @@ from homeassistant.components.config.customize import (
     CONFIG_PATH as CUSTOMIZE_CONFIG_PATH)
 import homeassistant.scripts.check_config as check_config
 
-from tests.common import get_test_config_dir, get_test_home_assistant
+from tests.common import (
+    get_test_config_dir, get_test_home_assistant, patch_yaml_files)
 
 CONFIG_DIR = get_test_config_dir()
 YAML_PATH = os.path.join(CONFIG_DIR, config_util.YAML_CONFIG_FILE)
@@ -550,6 +553,30 @@ class TestConfig(unittest.TestCase):
         ).result() == 'bad'
 
 
+@asynctest.mock.patch('homeassistant.config.os.path.isfile',
+                      mock.Mock(return_value=True))
+async def test_async_hass_config_yaml_merge(merge_log_err, hass):
+    """Test merge during async config reload."""
+    config = {
+        config_util.CONF_CORE: {config_util.CONF_PACKAGES: {
+            'pack_dict': {
+                'input_boolean': {'ib1': None}}}},
+        'input_boolean': {'ib2': None},
+        'light': {'platform': 'test'}
+    }
+
+    files = {config_util.YAML_CONFIG_FILE: yaml.dump(config)}
+    with patch_yaml_files(files, True):
+        conf = await config_util.async_hass_config_yaml(hass)
+
+    assert merge_log_err.call_count == 0
+    assert conf[config_util.CONF_CORE].get(config_util.CONF_PACKAGES) \
+        is not None
+    assert len(conf) == 3
+    assert len(conf['input_boolean']) == 2
+    assert len(conf['light']) == 1
+
+
 # pylint: disable=redefined-outer-name
 @pytest.fixture
 def merge_log_err(hass):