diff --git a/types/options.go b/types/options.go
index 007c5288bf..a0bda26bf3 100644
--- a/types/options.go
+++ b/types/options.go
@@ -278,6 +278,9 @@ func ReloadConfigurationFile(configFile string, storeOptions *StoreOptions) {
 		fmt.Printf("Failed to parse %s %v\n", configFile, err.Error())
 		return
 	}
+
+	// Clear storeOptions of previos settings
+	storeOptions = StoreOptions{}
 	if config.Storage.Driver != "" {
 		storeOptions.GraphDriverName = config.Storage.Driver
 	}
@@ -338,13 +341,13 @@ func ReloadConfigurationFile(configFile string, storeOptions *StoreOptions) {
 	if err != nil {
 		fmt.Print(err)
 	} else {
-		storeOptions.UIDMap = append(storeOptions.UIDMap, uidmap...)
+		storeOptions.UIDMap = uidmap
 	}
 	gidmap, err := idtools.ParseIDMap([]string{config.Storage.Options.RemapGIDs}, "remap-gids")
 	if err != nil {
 		fmt.Print(err)
 	} else {
-		storeOptions.GIDMap = append(storeOptions.GIDMap, gidmap...)
+		storeOptions.GIDMap = gidmap
 	}
 	storeOptions.RootAutoNsUser = config.Storage.Options.RootAutoUsernsUser
 	if config.Storage.Options.AutoUsernsMinSize > 0 {
@@ -356,8 +359,8 @@ func ReloadConfigurationFile(configFile string, storeOptions *StoreOptions) {
 
 	storeOptions.GraphDriverOptions = append(storeOptions.GraphDriverOptions, cfg.GetGraphDriverOptions(storeOptions.GraphDriverName, config.Storage.Options)...)
 
-	if os.Getenv("STORAGE_OPTS") != "" {
-		storeOptions.GraphDriverOptions = append(storeOptions.GraphDriverOptions, strings.Split(os.Getenv("STORAGE_OPTS"), ",")...)
+	if opts, ok := os.LookupEnv("STORAGE_OPTS"); ok {
+		storeOptions.GraphDriverOptions = strings.Split(opts, ",")
 	}
 	if len(storeOptions.GraphDriverOptions) == 1 && storeOptions.GraphDriverOptions[0] == "" {
 		storeOptions.GraphDriverOptions = nil