diff --git a/cmd/config.go b/cmd/config.go
index ce8ebdb7..3812d692 100644
--- a/cmd/config.go
+++ b/cmd/config.go
@@ -44,8 +44,11 @@ func addConfigFlags(flags *pflag.FlagSet) {
 	flags.Bool("branding.disableExternal", false, "disable external links such as GitHub links")
 }
 
-func getAuthentication(flags *pflag.FlagSet) (settings.AuthMethod, auth.Auther) {
+func getAuthentication(flags *pflag.FlagSet, defaults ...*settings.Settings) (settings.AuthMethod, auth.Auther) {
 	method := settings.AuthMethod(mustGetString(flags, "auth.method"))
+	if len(defaults) > 0 {
+		method = defaults[0].AuthMethod
+	}
 
 	var auther auth.Auther
 	if method == auth.MethodProxyAuth {
diff --git a/cmd/config_set.go b/cmd/config_set.go
index 5b417140..e1ffb6e5 100644
--- a/cmd/config_set.go
+++ b/cmd/config_set.go
@@ -71,6 +71,10 @@ you want to change. Other options will remain unchanged.`,
 		} else {
 			auther, err = d.store.Auth.Get(set.AuthMethod)
 			checkErr(err)
+			// check if there are new flags for existing auth method
+			set.AuthMethod, auther = getAuthentication(flags, set)
+			err = d.store.Auth.Save(auther)
+			checkErr(err)
 		}
 
 		err = d.store.Settings.Save(set)