Have you ever been to a Whole Foods before? I've been tons of times and I
still feel like Alice in Wonderland.
Are you going for lunch, or just for grocery shopping, or both?
In any case, their produce tends to be widely varied and outstanding. Can't go wrong with fruits and vegetables, and you could easily spend half an hour acquainting yourself with their selection (at least at the stores I've visited).
Although it is scandalously expensive, their salad and prepared foods bars are pretty outstanding, and I think most of the dishes (except desserts, of course) would be considered "clean" - if you avoid the obviously fried foods. The store in my neighborhood (in Maryland, now) has global cuisine, and pretty passable Indian food. My SO reports that their sushi is good. I am partial to the curried tempeh salad, sesame glazed tofu, and various veggie and fruit dishes.
The store in Austin has a chocolate kiosk with fountains of dark and milk chocolate, and all kinds of delightful things dipped in chocolate, like strawberries, bananas, handmade marshmallows, cookies, bits of cake, etc. They also have chunks of chocolate of all varieties stacked up in towers of deliciousness all around the kiosk. I still have dreams about it. Ummm...I guess if you're on an eat-clean challenge, you should stay away from there!
Hmmm...maybe I need to go to Whole Foods myself?
Be warned: Whole Foods' nickname is "Whole Paycheck"!