I had read about this place on happycow and decided to stop in on my San Francisco trip 2 weeks ago. Here's my Alameda Natural Grocery review.
The set up is very interesting. The store shares a building (one big roof) with other several businesses (bakery, coffee shop, sushi bar, and others). You find your way into the grocery store area and then you can take what you'd like and pay at the register. The selection is good, has all the usual natural grocery that I like: fresh produce, natural food brands, and such.