diff --git a/sphinx/application.py b/sphinx/application.py
index 68edd588c..fe2990836 100644
--- a/sphinx/application.py
+++ b/sphinx/application.py
@@ -74,10 +74,7 @@ class Sphinx(object):
         self._events = events.copy()
 
         # read config
-        self.config = Config(confdir, 'conf.py')
-        if confoverrides:
-            for key, val in confoverrides.items():
-                setattr(self.config, key, val)
+        self.config = Config(confdir, 'conf.py', confoverrides)
 
         # load all extension modules
         for extension in self.config.extensions:
@@ -86,6 +83,9 @@ class Sphinx(object):
         if self.config.setup:
             self.config.setup(self)
 
+        # now that we know all config values, collect them from conf.py
+        self.config.init_values()
+
         if buildername is None:
             print >>status, 'No builder selected, using default: html'
             buildername = 'html'
@@ -176,10 +176,9 @@ class Sphinx(object):
         self.builderclasses[builder.name] = builder
 
     def add_config_value(self, name, default, rebuild_env):
-        if name in self.config.valuenames:
+        if name in self.config.config_values:
             raise ExtensionError('Config value %r already present' % name)
-        self.config.valuenames.add(name)
-        self.config.__class__.config_values[name] = (default, rebuild_env)
+        self.config.config_values[name] = (default, rebuild_env)
 
     def add_event(self, name):
         if name in self._events:
diff --git a/sphinx/config.py b/sphinx/config.py
index dd6d12651..024a7f868 100644
--- a/sphinx/config.py
+++ b/sphinx/config.py
@@ -30,11 +30,7 @@ class Config(object):
         today = ('', True),
         today_fmt = ('%B %d, %Y', True),
 
-        # extensibility
-        templates_path = ([], False),
-        extensions = ([], True),
-
-        # general reading options
+        # general options
         master_doc = ('contents', True),
         source_suffix = ('.rst', True),
         unused_docs = ([], True),
@@ -44,6 +40,7 @@ class Config(object):
         add_module_names = (True, True),
         show_authors = (False, True),
         pygments_style = ('sphinx', False),
+        templates_path = ([], False),
         template_bridge = (None, False),
 
         # HTML options
@@ -80,8 +77,8 @@ class Config(object):
         latex_use_modindex = (True, False),
     )
 
-    def __init__(self, dirname, filename):
-        self.valuenames = set(self.config_values.keys())
+    def __init__(self, dirname, filename, overrides):
+        self.overrides = overrides
         config = {'__file__': path.join(dirname, filename)}
         olddir = os.getcwd()
         try:
@@ -89,15 +86,24 @@ class Config(object):
             execfile(config['__file__'], config)
         finally:
             os.chdir(olddir)
-        for name in config:
-            if name in self.valuenames:
-                self.__dict__[name] = config[name]
+        self._raw_config = config
+        # these two must be preinitialized because extensions can add their
+        # own config values
         self.setup = config.get('setup', None)
+        self.extensions = config.get('extensions', [])
+
+    def init_values(self):
+        config = self._raw_config
+        config.update(self.overrides)
+        for name in self._raw_config:
+            if name in self.config_values:
+                self.__dict__[name] = config[name]
+        del self._raw_config
 
     def __getattr__(self, name):
         if name.startswith('_'):
             raise AttributeError(name)
-        if name not in self.valuenames:
+        if name not in self.config_values:
             raise AttributeError('No such config value: %s' % name)
         default = self.config_values[name][0]
         if callable(default):
@@ -114,4 +120,4 @@ class Config(object):
         delattr(self, name)
 
     def __contains__(self, name):
-        return name in self.valuenames
+        return name in self.config_values
diff --git a/sphinx/environment.py b/sphinx/environment.py
index 8b3bca4a8..f1adf6ea6 100644
--- a/sphinx/environment.py
+++ b/sphinx/environment.py
@@ -397,9 +397,7 @@ class BuildEnvironment:
             for key, descr in config.config_values.iteritems():
                 if not descr[1]:
                     continue
-                if not hasattr(self.config, key) or \
-                   self.config[key] != config[key]:
-
+                if self.config[key] != config[key]:
                     msg = '[config changed] '
                     config_changed = True
                     break