diff --git a/qutebrowser/config/config.py b/qutebrowser/config/config.py
index be8aee85d..baadf1cfa 100644
--- a/qutebrowser/config/config.py
+++ b/qutebrowser/config/config.py
@@ -414,10 +414,8 @@ class Config(QObject):
         If save_yaml=True is given, also remove all customization from the YAML
         file.
         """
-        # FIXME:conf support per-URL settings?
-        old_values = self._values
-        self._values = {}
-        for name in old_values:
+        for name, values in self._values.items():
+            values.clear()
             self.changed.emit(name)
 
         if save_yaml:
diff --git a/qutebrowser/config/configfiles.py b/qutebrowser/config/configfiles.py
index 91735f536..f2e104c05 100644
--- a/qutebrowser/config/configfiles.py
+++ b/qutebrowser/config/configfiles.py
@@ -239,8 +239,8 @@ class YamlConfig(QObject):
 
     def clear(self):
         """Clear all values from the YAML file."""
-        # FIXME:conf per-URL support?
-        self._values = []
+        for values in self._values.values():
+            values.clear()
         self._mark_changed()
 
 
diff --git a/qutebrowser/config/configutils.py b/qutebrowser/config/configutils.py
index 8b5593749..c915b7674 100644
--- a/qutebrowser/config/configutils.py
+++ b/qutebrowser/config/configutils.py
@@ -90,6 +90,10 @@ class Values:
         # FIXME:conf Should this ignore patterns which weren't found?
         self._values = [v for v in self._values if v.pattern != pattern]
 
+    def clear(self):
+        """Clear all customization for this value."""
+        self._values = []
+
     def _get_fallback(self):
         """Get the fallback global/default value."""
         if self._values: