Macrobiótica Vida Natural Atenas - closest health food store that will have a decent selection of product snot foundin Auto-Mercado
Green Center Organic Super Market - this is the ultimate “Whole Foods” of Costa Rica. You will usually find almost everything here that you can’t in other stores. Yes, it’s pricey, and yes, it’s not quite Whole Foods :)
Nueces Industriales - Almonds, Walnuts, Cashews, Hazelnuts, etc. All kind of nuts in bulk quantities and excellent prices. Go here once every month or so and stock up on all your nutty needs.
Don Luis Panes - Gluten Free bakery with excellent bread.
EcoPlaza - Nice plaza with many eco-friendly stores and a couple of restaurants
Cúrcuma - for all your spices needs, almost everything here you’ll need, though a bit pricey.
El Tramito a Granel Escazu - assortment of spices, salts, grains and everything you need to cook, bake, season and even eat at once is overwhelming. Great for buying things in bulk. They also do deliveries though “encomienda” on the buses.