diff --git a/qmk_cli/subcommands/setup.py b/qmk_cli/subcommands/setup.py
index 9d30265..9a006c6 100644
--- a/qmk_cli/subcommands/setup.py
+++ b/qmk_cli/subcommands/setup.py
@@ -87,6 +87,7 @@ def setup(cli):
     # Offer to set `user.qmk_home` for them.
     if str(cli.args.home) != os.environ['QMK_HOME'] and yesno(home_prompt):
         cli.config['user']['qmk_home'] = str(cli.args.home.absolute())
+        cli.config_source['user']['qmk_home'] = 'config_file'
         cli.write_config_option('user', 'qmk_home')
 
     # Run `qmk doctor` to check the rest of the environment out