diff --git a/qutebrowser/config/configfiles.py b/qutebrowser/config/configfiles.py
index f9a36ea31..62e4d7970 100644
--- a/qutebrowser/config/configfiles.py
+++ b/qutebrowser/config/configfiles.py
@@ -80,7 +80,7 @@ class YamlConfig(QObject):
         VERSION: The current version number of the config file.
     """
 
-    VERSION = 1
+    VERSION = 2
     changed = pyqtSignal()
 
     def __init__(self, parent=None):
@@ -173,9 +173,12 @@ class YamlConfig(QObject):
 
         config_version = self._pop_object(yaml_data, 'config_version', int)
 
-        settings = self._load_settings_object(yaml_data)
-
-        self._dirty = False
+        if config_version == 1:
+            settings = self._load_legacy_settings_object(yaml_data)
+            self._mark_changed()
+        else:
+            settings = self._load_settings_object(yaml_data)
+            self._dirty = False
         settings = self._handle_migrations(settings)
         self._validate(settings)
         self._build_values(settings)
@@ -184,9 +187,15 @@ class YamlConfig(QObject):
         """Load the settings from the settings: key."""
         return self._pop_object(yaml_data, 'settings', dict)
 
+    def _load_legacy_settings_object(self, yaml_data):
+        data = self._pop_object(yaml_data, 'global', dict)
+        settings = {}
+        for name, value in data.items():
+            settings[name] = {'global': value}
+        return settings
+
     def _build_values(self, settings):
         """Build up self._values from the values in the given dict."""
-        # FIXME:conf test this
         for name, yaml_values in settings.items():
             values = configutils.Values(configdata.DATA[name])
             if 'global' in yaml_values:
@@ -200,9 +209,6 @@ class YamlConfig(QObject):
 
     def _handle_migrations(self, settings):
         """Migrate older configs to the newest format."""
-        # FIXME:conf handle per-URL settings
-        # FIXME:conf migrate from older format with global: key
-
         # Simple renamed/deleted options
         for name in list(settings):
             if name in configdata.MIGRATIONS.renamed:
diff --git a/tests/unit/config/test_configfiles.py b/tests/unit/config/test_configfiles.py
index d7d0b6173..29314d87e 100644
--- a/tests/unit/config/test_configfiles.py
+++ b/tests/unit/config/test_configfiles.py
@@ -45,19 +45,25 @@ class AutoConfigHelper:
     def __init__(self, config_tmpdir):
         self.fobj = config_tmpdir / 'autoconfig.yml'
 
-    def write(self, values):
-        data = {'config_version': 1, 'settings': values}
+    def write_toplevel(self, data):
         with self.fobj.open('w', encoding='utf-8') as f:
             utils.yaml_dump(data, f)
 
+    def write(self, values):
+        data = {'config_version': 2, 'settings': values}
+        self.write_toplevel(data)
+
     def write_raw(self, text):
         self.fobj.write_text(text, encoding='utf-8', ensure=True)
 
-    def read(self):
+    def read_toplevel(self):
         with self.fobj.open('r', encoding='utf-8') as f:
             data = utils.yaml_load(f)
-            assert data['config_version'] == 1
-            return data['settings']
+            assert data['config_version'] == 2
+            return data
+
+    def read(self):
+        return self.read_toplevel()['settings']
 
     def read_raw(self):
         return self.fobj.read_text('utf-8')
@@ -284,9 +290,9 @@ class TestYaml:
 
     @pytest.mark.parametrize('line, text, exception', [
         ('%', 'While parsing', 'while scanning a directive'),
-        ('settings: 42\nconfig_version: 1',
+        ('settings: 42\nconfig_version: 2',
          'While loading data', "'settings' object is not a dict"),
-        ('foo: 42\nconfig_version: 1', 'While loading data',
+        ('foo: 42\nconfig_version: 2', 'While loading data',
          "Toplevel object does not contain 'settings' key"),
         ('settings: {}', 'While loading data',
          "Toplevel object does not contain 'config_version' key"),
@@ -304,6 +310,26 @@ class TestYaml:
         assert str(error.exception).splitlines()[0] == exception
         assert error.traceback is None
 
+    def test_legacy_migration(self, yaml, autoconfig, qtbot):
+        autoconfig.write_toplevel({
+            'config_version': 1,
+            'global': {'content.javascript.enabled': True},
+        })
+        with qtbot.wait_signal(yaml.changed):
+            yaml.load()
+
+        yaml._save()
+
+        data = autoconfig.read_toplevel()
+        assert data == {
+            'config_version': 2,
+            'settings': {
+                'content.javascript.enabled': {
+                    'global': True,
+                }
+            }
+        }
+
     def test_oserror(self, yaml, autoconfig):
         autoconfig.fobj.ensure()
         autoconfig.fobj.chmod(0)
diff --git a/tests/unit/config/test_configinit.py b/tests/unit/config/test_configinit.py
index 230b64a54..c139ff6b9 100644
--- a/tests/unit/config/test_configinit.py
+++ b/tests/unit/config/test_configinit.py
@@ -123,19 +123,19 @@ class TestEarlyInit:
                 'settings:',
                 '  colors.foobar:',
                 '    global: magenta',
-                'config_version: 1',
+                'config_version: 2',
             ],
             'wrong-type': [
                 'settings:',
                 '  tabs.position:',
                 '    global: true',
-                'config_version: 1',
+                'config_version: 2',
             ],
             False: [
                 'settings:',
                 '  colors.hints.fg:',
                 '    global: magenta',
-                'config_version: 1',
+                'config_version: 2',
             ],
         }
         text = '\n'.join(yaml_lines[invalid_yaml])
@@ -240,7 +240,7 @@ class TestEarlyInit:
             args.temp_settings = settings
         elif method == 'auto':
             autoconfig_file = config_tmpdir / 'autoconfig.yml'
-            lines = (["config_version: 1", "settings:"] +
+            lines = (["config_version: 2", "settings:"] +
                      ["  {}:\n    global:\n      '{}'".format(k, v)
                       for k, v in settings])
             autoconfig_file.write_text('\n'.join(lines), 'utf-8', ensure=True)