When I need organic vegetables right away and can`t wait a week for the next delivery (or the next Farmer`s Market) I head to the closest organic shops in Tokyo. Here are my favorite with online options:
1) Precce & Tokyu Stores have a small organic section. Just look for the JAS organic sign above.
Precce Website: http://shop.tokyu-bell.jp/tokyu-store/app/common/index (in Japanese)
Tokyu Website: http://www.tokyu-bell.jp/ (in Japanese)
Locations: Tokyo and surrounding areas
Website: http://www.oisix.com (in Japanese)
Locations: Futakotamagawa Rise – B1 level, Kichijoji – B1 in the Atre Building, Ebisu Mitsukoshi, Nakameguro Tokyu Store, Meguro Precce Store, Sangenjaya Tokyu Store, etc. Full list here.
4) Crayon House All in one shop (veggies, restaurant, cosmetics, books & toys).
Another resource for fresh, organic food are the Tokyo Area Farmer`s Markets. Here is a list from the archives. ** Ask for “Yuuki” (有機) which means Organic in Japanese. **
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