diff --git a/api/cmd/portainer/main.go b/api/cmd/portainer/main.go
index 85c1f586b..95adf5c7c 100644
--- a/api/cmd/portainer/main.go
+++ b/api/cmd/portainer/main.go
@@ -107,11 +107,6 @@ func initDataStore(flags *portainer.CLIFlags, secretKey []byte, fileService port
 	if isNew {
 		// from MigrateData
 		store.VersionService.StoreDBVersion(portainer.DBVersion)
-
-		err := updateSettingsFromFlags(store, flags)
-		if err != nil {
-			log.Fatalf("Failed updating settings from flags: %v", err)
-		}
 	} else {
 		storedVersion, err := store.VersionService.DBVersion()
 		if err != nil {
@@ -125,6 +120,11 @@ func initDataStore(flags *portainer.CLIFlags, secretKey []byte, fileService port
 		}
 	}
 
+	err = updateSettingsFromFlags(store, flags)
+	if err != nil {
+		log.Fatalf("Failed updating settings from flags: %v", err)
+	}
+
 	// this is for the db restore functionality - needs more tests.
 	go func() {
 		<-shutdownCtx.Done()