Order the items with the same logic as the one used on the web app. If the alphabetical method is set on the site preferences, use it on the app too.
It should be alphabetical on the iPhone app. It’s not for you?
The website offers two ordering options; purely alphabetical & by popularity. I think the iPhone app only offers alphabetical ordering, right?
My suggestion is that both the website and the app should use the same ordering. Changing it on one side should be carried over to the other end.