When it's not Farmer's Market season, I often head to the Natural Food Depot as well.
For a selection of smaller stores, you could try Kingston Road west of Victoria Park. There is a butcher that carries natural and organic meats (Close to the Bone), a health food store (Loving Nature), a market with local produce (Courage Foods) and even a video store (Movies 2 Go) that sells items from the family farm like apples, pumpkins and maple syrup!
Not certified organic, and in East York, but if you can't find anything better closer to home, you could try "Fresh from the Farm" near Donlands and O'Connor. http://freshfromthefarm.ca/. All Kitchener-Waterloo area Mennonite products. Mennonite farmers produce food for their local community, and since they trust each other to use healthy practices, they don't feel the need to certify. Good stuff, available in store or by pre-order. Also baked goods, home canning, cheese, eggs and produce (in season).
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