diff --git a/qutebrowser/config/configcommands.py b/qutebrowser/config/configcommands.py
index 5249ca778..6c2880100 100644
--- a/qutebrowser/config/configcommands.py
+++ b/qutebrowser/config/configcommands.py
@@ -269,8 +269,11 @@ class ConfigCommands:
             options = [(opt, opt.default)
                        for _name, opt in sorted(configdata.DATA.items())]
             bindings = dict(configdata.DATA['bindings.default'].default)
+            commented = True
         else:
             options = list(self._config)
             bindings = dict(self._config.get_obj('bindings.commands'))
+            commented = False
 
-        configfiles.write_config_py(filename, options, bindings)
+        configfiles.write_config_py(filename, options, bindings,
+                                    commented=commented)
diff --git a/qutebrowser/config/configfiles.py b/qutebrowser/config/configfiles.py
index c23e616a0..0aa61c149 100644
--- a/qutebrowser/config/configfiles.py
+++ b/qutebrowser/config/configfiles.py
@@ -245,45 +245,59 @@ class ConfigAPI:
             self._keyconfig.unbind(key, mode=mode)
 
 
-def write_config_py(filename, options, bindings):
+def write_config_py(filename, options, bindings, *, commented):
     """Write a config.py file from given values."""
+    c = '#' if commented else ''
+    cs = '# ' if commented else ''
     with open(filename, 'w', encoding='utf-8') as f:
-        f.write("# Autogenerated config.py - please remove lines you don't "
-                "customize!\n")
-        f.write("# Documentation:\n")
-        f.write("#   qute://help/configuring.html\n")
-        f.write("#   qute://help/settings.html\n\n")
+        f.write(c + "# Autogenerated config.py\n")
+        f.write(c + "# Documentation:\n")
+        f.write(c + "#   qute://help/configuring.html\n")
+        f.write(c + "#   qute://help/settings.html\n\n")
+        if commented:
+            # When generated from an autoconfig.yml with commented=False,
+            # we don't want to load that autoconfig.yml anymore.
+            f.write("## This is here so configs done via the GUI are still "
+                    "loaded.\n")
+            f.write("## Remove it to not load settings done via the GUI.\n")
+            f.write("config.load_autoconfig()\n\n")
+        else:
+            f.write("# Uncomment this to still load settings configured via "
+                    "autoconfig.yml\n")
+            f.write("# config.load_autoconfig()\n\n")
 
         for opt, value in options:
             if opt.name in ['bindings.commands', 'bindings.default']:
                 continue
 
             for line in textwrap.wrap(opt.description):
-                f.write('# {}\n'.format(line))
+                f.write(c + "# {}\n".format(line))
 
-            f.write('# Type: {}\n'.format(opt.typ.get_name()))
+            f.write(c + "# Type: {}\n".format(opt.typ.get_name()))
 
             valid_values = opt.typ.get_valid_values()
             if valid_values is not None and valid_values.generate_docs:
-                f.write("# Valid values:\n")
+                f.write(c + "# Valid values:\n")
                 for val in valid_values:
                     try:
                         desc = valid_values.descriptions[val]
-                        f.write("#   - {}: {}".format(val, desc) + "\n")
+                        f.write(c + "#   - {}: {}".format(val, desc) + "\n")
                     except KeyError:
-                        f.write("#   - {}".format(val) + "\n")
+                        f.write(c + "#   - {}".format(val) + "\n")
 
-            f.write('c.{} = {!r}\n\n'.format(opt.name, value))
+            f.write(cs + 'c.{} = {!r}\n\n'.format(opt.name, value))
 
         normal_bindings = bindings.pop('normal', {})
-        f.write('# Bindings for normal mode\n')
+        if normal_bindings:
+            f.write(c + '# Bindings for normal mode\n')
         for key, command in sorted(normal_bindings.items()):
-            f.write('config.bind({!r}, {!r})\n'.format(key, command))
+            f.write(cs + 'config.bind({!r}, {!r})\n'.format(key, command))
 
         for mode, mode_bindings in sorted(bindings.items()):
-            f.write('\n# Bindings for {} mode\n'.format(mode))
+            f.write('\n')
+            f.write(c + '# Bindings for {} mode\n'.format(mode))
             for key, command in sorted(mode_bindings.items()):
-                f.write('config.bind({!r}, {!r}, mode={!r})\n'.format(
+                f.write(cs + 'config.bind({!r}, {!r}, mode={!r})\n'.format(
                     key, command, mode))