diff --git a/waflib/Configure.py b/waflib/Configure.py
index 298198d0..aefdaf16 100644
--- a/waflib/Configure.py
+++ b/waflib/Configure.py
@@ -169,6 +169,7 @@ class ConfigurationContext(Context.Context):
 		env = ConfigSet.ConfigSet()
 		env['argv'] = sys.argv
 		env['options'] = Options.options.__dict__
+		env['config_cmd'] = self.cmd
 
 		env.run_dir = Context.run_dir
 		env.top_dir = Context.top_dir
diff --git a/waflib/Scripting.py b/waflib/Scripting.py
index 1842bd6b..bd217e3f 100644
--- a/waflib/Scripting.py
+++ b/waflib/Scripting.py
@@ -583,12 +583,15 @@ def autoconfigure(execute_method):
 				do_config = h != env.hash
 
 		if do_config:
-			Options.commands.insert(0, self.cmd)
-			Options.commands.insert(0, 'configure')
 			if Configure.autoconfig == 'clobber':
+				tmp = Options.options.__dict__
 				Options.options.__dict__ = env.options
-			return
-
+				try:
+					run_command(env['config_cmd'])
+				finally:
+					Options.options.__dict__ = tmp
+			else:
+				run_command(env['configure'])
 		return execute_method(self)
 	return execute
 Build.BuildContext.execute = autoconfigure(Build.BuildContext.execute)