Organic Food Stores and Markets in Tokyo

Poste date: Friday, December 2, 2022

Although there aren’t as many organic stores in Japan as there are in the United States and Europe, the number is gradually increasing. People are becoming more sensitive to how food is grown or raised because it can have a major impact on mental and emotional health.

More and more organic supermarkets, farmers markets, restaurants, and cafes are opening in Japan. And young, trendy Tokyoites have found the appeal of going organic during their lunch breaks.

Buying Organic Food in Japanese Supermarkets

Several supermarkets across Japan, and more specifically Tokyo, have begun stocking organic food. Seijo Ishii, for example, is a chain of premium grocery stores focusing on foreign imports as well as organic products. Some major supermarkets like Aeon have organic vegetable sections. Look out for the words 'オーガニック(organic)' or '無農薬(pesticide-free)' in Japanese. 

Organic Stores in Tokyo

Here are some major organic shops in Tokyo. Please note that all websites are in Japanese.

Natural House

Natural House has several shops in Tokyo. As far as niche markets go, Natural House is likely going to have the best selection around. They do have a small skincare, cosmetics, and perfume section, as well as a hot deli bar serving a rotating mix of sustainable vegetarian and vegan-friendly options. Please visit their website to find shop addresses.

Online Store

Crayon House

Crayon House is a funky spot that can turn into an afternoon of fun for the whole family! They have a children’s bookstore on the first floor, as well as an entire floor of wooden toys one story up. The basement floor is dedicated to organic products. Crayon House also has a location in Osaka.

A: 3-8-15 Kita-Aoyama Minato-ku Tokyo

Online Store

Horizon Farms

Horizon Farms provides safe, organic, natural, high-quality and sustainable meat, fruit, groceries and other agricultural products. Dairy-free and vegetarian products are also available.

You can also shop via Amazon Japan


OHSAWA JAPAN is one of the coolest spots for organic food in Tokyo. The store is dedicated to macrobiotic cuisine and lifestyles, with a dedicated macrobiotic deli. Not only can you buy organic ingredients, but you’ll find an excellent range of gluten-free goods and baking ingredients, suited for home chefs and novices alike.

A: CI Building Higashiyama Store: 3-1-6 Higashiyama, Meguro-ku

Online Store LIMA Netshop

Bio c’ Bon

Bio c’ Bon is a French grocery store chain specializing in French import goods and other specialty foods. They also have one of the best bulk sections in Tokyo, with everything from carob chips to steel-cut oats to dried fruit. Bio c’ Bon also has a hot deli and salad bar with a selection of fresh cheeses and breads as well as vegan hot deli options. Please find shop addresses on their website

Online Store

自然食品 F&F

F&F has exploded over the last few years, quickly becoming the most easily reachable store on the list. Their locations extend into outside of Tokyo (Kanagawa, Chiba, Saitama).

Online Store


Tucked away in the quiet yet enviable neighborhood of Yoyogi-Uehara, this sweet neighborhood favorite has been serving health-conscious Tokyoites for years. They have an excellent organic produce section, and they focus primarily on patrons looking for macrobiotic food options.

Ochanomizu Shop
A: 3-3-13, Kanda Surugadai, Chiyoda-ku, Tokyo

Yoyogi Uehara Shop
A: 3-23-6 Nishihara, Shibuya-ku, Tokyo

Online Store

Farmers Markets in Tokyo

Hills Marche

Hills Marche is held in the trendy business district of Akasaka, in the heart of Tokyo. Located in the Ark Hills complex, it runs every Saturday from 10 a.m., offering everything from organic, fresh produce to kids cooking classes. While a little out of the way for those not located inside the Ark Hills complex, it’s a wonderful, old fashioned market with lots to do — take the kids and make a day of it.

A: 1-12-32 Akasaka Minato-ku Tokyo
D: Saturdays: 10:00 - 14:00

UNU Farmers market

This farmers market is probably the most famous of the bunch in Tokyo. Located in front of the United Nations University campus, it’s a wonderful way to spend a sunny spring morning. Open both Saturdays and Sundays, the UNU Farmers Market is excellent for those who may not get a full weekend off but still need to do a full week’s shopping. It’s also open two hours later than the Akasaka farmers market and is quite a bit larger (though selection always depends on the week and season).

A: 5-53-70 Jingumae Shibuya-ku Tokyo
D: Saturdays & Sunday: 10:00 - 16:00

Yebisu Marche

Yebisu Marche is small but mighty, and by far the most conveniently located of the markets on our list — right on the platform outside of Ebisu Station. Organized by the Marche Japan organization (which organizes farmers markets all over the country), its focus is on fresh produce grown in and around Tokyo.

A: Yebisu Garden Place  1-13-1, Mita, Meguro-ku, Tokyo
D: Sundays: 11:00 - 17:00

Shopping Online for Organic Food in Japan

Sometimes, your busy Japan life doesn’t allow you the time to go out and enjoy a leisurely farmers market stroll, or you may be located too far away for it to be worth the trip. The wide distribution capabilities of cold shipping have made it possible for organic veggies and other products to be distributed throughout the country. Below are a few online shops that cater to organic-minded clientele. Please note that all the shops mentioned above also have an online shop.

Read More: Online Grocery Shopping in Japan

Amazon Japan

In addition to the regular Amazon shop, Amazon Japan offers organic vegetables on Amazon Fresh.

Bio Marche

Bio Marche comes from the French shorthand for organic, and is one of the biggest distributors of organic and natural foods in Japan. The service runs on a regular schedule, where you receive a delivery once a week on a set date, similar to a CSA.


For anyone wanting to eat healthy, we recommend including organic Japanese ingredients in your diet. Lucky for expats, the country has really begun to focus on natural farming methods, with a new push for wider availability. For more helpful information on food in Japan, check out our comprehensive guides that cover everything from catering options, to etiquette and important vocabulary to keep you and your loved ones safe. Please visit Best Vegan / Vegetarian Restaurants in Tokyo if you would like to eat out.