Choosing an organic restaurant in Tokyo can feel overwhelming. The city offers a wide range of options: restaurants specializing in organic vegetables, those committed to natural farming methods, and establishments serving sustainable seafood. The term “organic” itself means different things to different restaurants.
Some hold third-party certifications. Others operate under their own standards. Not all ingredients are organic at every location, and some restaurants focus on specific categories rather than comprehensive coverage.
This guide organizes information about restaurants in Tokyo that identify as “organic” or “sustainable.” It presents their characteristics and practices without making recommendations. The goal is to help you decide which restaurants align with your values and needs.
How We Selected These Restaurants
We researched restaurants based on the following criteria. These are organizational filters, not rankings:
- Official websites explicitly mention “organic,” “natural farming,” or “sustainable”
- Third-party certifications (such as JAS Organic Restaurant Standards or Leafers certification) are documented, or independent cultivation and sourcing standards are publicly disclosed
- Information about ingredient origins, producers, and cultivation methods is available
9 Organic Restaurants in Tokyo
1. Crayon House Organic Restaurant “Hiroba”
Location: Kichijoji
Restaurant Profile: One of the first restaurants to receive JAS Organic Restaurant certification under Japan’s national standards. Lunch is served buffet-style featuring organic vegetables that change daily. Dinner offers course menus and à la carte options. The restaurant aims to connect producers with consumers, functioning as a meeting place to expand organic agriculture.
Certification and Standards: Holds JAS Organic Restaurant certification. Organic ingredient management and record-keeping follow this national standard. Storage, cooking, and washing processes are formalized and subject to third-party audits.
Restaurant-Specific Practices and Transparency: Discloses the origin and producers of vegetables used, along with the ingredients in seasonings and processed foods. If certain organic ingredients are unavailable and conventional alternatives are used, this is openly posted. The restaurant encourages customers to reduce food waste and composts kitchen scraps using an on-site processor.
Who This Restaurant Suits: People with allergies or concerns about additives who want full ingredient transparency. Families with young children seeking reassurance about food safety. Those who prioritize third-party certification and clear management systems for organic ingredients.
Considerations: Because of the buffet format, complete prevention of cross-contamination for specific allergen removal may not be guaranteed (inquiries recommended). Specific percentages of organic ingredient procurement are not published. Operating hours, holidays, reservation methods, and price ranges are not fully detailed on the official website.
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2. Ristorante Acquapazza
Location: Gaienmae
Restaurant Profile: Focuses on “delicious Italian cuisine using Japanese ingredients.” The restaurant sources safe, high-quality ingredients from Japanese producers and prepares them using Italian techniques. It holds both Leafers organic restaurant certification (private standard) and JAS Organic Restaurant certification (national standard).
Certification and Standards: Under JAS Organic Restaurant certification, measures are in place to prevent mixing of organic and non-organic ingredients.
Restaurant-Specific Practices and Transparency: Chef Yoshimi Hidaka personally visits production sites across Japan and builds relationships with trusted producers. The restaurant prioritizes domestic ingredients and structures its menu around Japan’s four seasons.
Who This Restaurant Suits: Those seeking organic cuisine for formal occasions such as business meals or anniversaries. People who want both the quality of Italian cooking and ingredient safety. Those who value the chef’s direct relationships with producers and site visits.
Considerations: If you want specific JAS-certified “organic course” options, advance confirmation and reservations are recommended. Specific percentages of organic ingredient procurement are not published. Operating hours, holidays, reservation methods, and price ranges are not fully detailed on the official website.
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Ikkyu
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3. WE ARE THE FARM
Locations: Azabu-Juban, Akasaka, Ebisu, Meguro, Shibuya, Toyosu
Restaurant Profile: Operating under the concept “ALL FARM,” this vegetable-focused restaurant cultivates its own fields, plants seeds, and grows produce without pesticides or chemical fertilizers. Vegetables are harvested each morning from the company’s farm in Sakura City, Chiba Prefecture, and delivered directly to the restaurants.
Certification and Standards: No third-party certification
Restaurant-Specific Practices and Transparency: The official website states that farming is done without pesticides or chemical fertilizers using outdoor cultivation methods (self-reported independent standards). The restaurant intentionally grows heirloom and fixed-seed varieties that are difficult to distribute commercially, offering diverse produce. To reduce food waste, the kitchen uses all vegetables including those that don’t meet standard appearance specifications. The restaurant also encourages customers to take leftovers home and has eliminated plastic straws.
Who This Restaurant Suits: People who want to eat large amounts of fresh vegetables with concentrated flavor. Those interested in unique, distinctive vegetables rather than uniform supermarket produce. People who connect with the farm-to-table business model.
Considerations: Available vegetables may change suddenly due to weather or harvest conditions. The restaurant does not hold third-party certifications such as organic JAS, and cultivation methods are based on self-reported independent standards. Operating hours, holidays, reservation methods, and price ranges are not fully detailed on the official website.
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4. Toyouke Organics Restaurant
Location: Yoga Station
Restaurant Profile: Connects farming with food under a concept of managing the entire process from cultivation to preparation. The restaurant operates large-scale farms in Hokkaido and Shizuoka, using saved seeds and natural farming methods (no pesticides or chemical fertilizers). This vertical integration covers production through restaurant service.
Certification and Standards: No third-party certification
Restaurant-Specific Practices and Transparency: States that it does not use pesticides, chemical fertilizers, chemical seasonings, food additives, or genetically modified crops, and emphasizes heirloom varieties, fixed seeds, and seed saving (self-reported independent standards). The menu centers on crops from the company’s farms grown using natural farming methods, with dishes focused on seasonal harvests. The philosophy prioritizes natural seeds and soil microorganisms in compost-based cultivation.
Who This Restaurant Suits: Those seeking standards stricter than typical “organic,” such as “natural farming” and “seed saving.” People who want to enjoy the authentic flavors of ingredients in traditional Japanese-style cuisine.
Considerations: Operating schedules may change due to the attached shop and events. The restaurant does not hold third-party certifications (such as organic JAS), and items listed as not used are based on self-reported independent standards. The parent organization is affiliated with a specific natural therapy advocacy group.
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5. MOMINOKI HOUSE
Location: Meiji-Jingumae
Restaurant Profile: A natural food restaurant operating since 1976, using naturally cultivated vegetables, brown rice, and additive-free seasonings to support the physical and mental health of diners. The concept is “gifts from nature,” maintained over decades of operation.
Certification and Standards: No third-party certification
Restaurant-Specific Practices and Transparency: Uses pesticide-free and organically grown vegetables from contract farms, along with completely pesticide-free rice (self-reported). States that sugar and chemical seasonings are not used, and genetically modified foods are excluded. Interior materials include diatomaceous earth and zelkova wood for environmental consideration. Based on its philosophy, the restaurant does not use microwave ovens and uses ionized water for cooking and drinking.
Who This Restaurant Suits: People practicing macrobiotic diets (though meat and fish options are available for dining companions). Those seeking a quiet, natural space in the Harajuku area.
Considerations: Does not hold third-party certification (such as organic JAS). The use of ionized water has limited scientific backing and is based on the restaurant’s independent philosophy.
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6. BROWN RICE
Location: Omotesando
Restaurant Profile: A vegan restaurant proposed by Neal’s Yard Remedies under the concept of “whole food.” The menu reflects Japan’s four seasons and aims to balance body and mind through beautiful, delicious Japanese cuisine. All menu items are vegan and contain no animal products.
Certification and Standards: No third-party certification
Restaurant-Specific Practices and Transparency: All seasonings including miso, pickles, and sesame salt are made in-house. The restaurant maintains long-term trust relationships with producers and sources ingredients at fair prices for continuous procurement. Environmental initiatives include composting some kitchen waste and using environmentally conscious materials and energy-efficient equipment in the restaurant design.
Who This Restaurant Suits: Vegans and vegetarians who avoid animal products. Those who connect with the worldview and aesthetic of Neal’s Yard Remedies.
Considerations: The menu does not include meat, fish, eggs, or dairy products. Allergy accommodations require individual confirmation. Does not hold third-party certification (such as organic JAS).
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7. Ginza KAZAN
Location: Ginza
Restaurant Profile: A seafood restaurant offering “healthy and sustainable” cuisine composed entirely of seafood and vegetables, with no meat. Operated directly by a seafood trading company, the restaurant sources high-quality seafood from around the world through its own networks.
Certification and Standards: The “Angel Shrimp” served is certified under France’s QUALICERT quality assurance standard and is raised without antibiotics.
Restaurant-Specific Practices and Transparency: Provides detailed traceability information about the growing environments of seafood (unpolluted waters, farming environments close to natural conditions) and safety.
Who This Restaurant Suits: People who dislike meat or follow pescatarian diets. Those looking for a formal dining venue in Ginza.
Considerations: No meat dishes are available given the menu structure. QUALICERT certification validity is subject to periodic renewal.
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Ikkyu
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8. Bombay Bazaar
Location: Daikanyama
Restaurant Profile: A landmark café and restaurant in Daikanyama offering homemade dishes using safe, reliable ingredients. One of the cafés holding JAS Organic Restaurant certification. Located in a distinctive underground space with high ceilings, attached to Blue Market (apparel).
Certification and Standards: Uses and manages organic ingredients under JAS Organic Restaurant certification.
Restaurant-Specific Practices and Transparency: Sources fresh ingredients through collaboration with farmers’ markets (including affiliated locations).
Who This Restaurant Suits: People who want healthy meals and desserts while shopping in Daikanyama. Those seeking authentic organic menus in a casual setting.
Considerations: Specific percentages of organic ingredient procurement are not published. Non-organic ingredients may be used when organic options are unavailable. Operating hours, holidays, reservation methods, and price ranges are not fully detailed on the official website.
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10. titi cafe
Location: Toshimaen
Restaurant Profile: Operating under the concept “value everyday meals,” this café occupies a renovated 60-year-old single-story house where a certified vegetable sommelier prepares food that nourishes body and mind. The café holds JAS Organic Restaurant certification and is certified by Nerima Ward as a partner in the “Delicious Clean Plate” program.
Certification and Standards: Ingredient management complies with JAS Organic Restaurant certification standards.
Restaurant-Specific Practices and Transparency: Uses vegetable peels and cores to make vegetable broth, reducing waste. Offers smaller portion sizes to help reduce leftovers.
Who This Restaurant Suits: People looking to address vegetable deficiencies through an everyday café. Those who want to dine in a relaxed, retro-style space.
Considerations: Operating days and hours may change, so checking social media or the official website in advance is recommended. Non-organic ingredients may be used when organic options are unavailable. Specific percentages of organic ingredient procurement are not published.
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Key Comparison Points
Third-Party Certification vs. Independent Standards
The restaurants listed include both those with national or international third-party certifications and those operating under independent standards. Third-party certification provides objective proof of management systems, but the absence of certification does not mean a restaurant is not sustainable. Some maintain rigorous independent standards. Others may not pursue certification due to costs or administrative burden.
Self-reported standards, however, have not undergone objective third-party verification. This distinction is less about trustworthiness and more about whether objective proof exists.
Types of Certifications and Their Meanings
- JAS Organic Restaurant Standards: Third-party certification based on national standards set by Japan’s Ministry of Agriculture, Forestry and Fisheries
- Leafers Certification: Private certification body
- MSC Certification: International certification for sustainable wild-caught fisheries
- ASC Certification: International evaluation of environmental and social standards in aquaculture
- QUALICERT: French quality assurance standard
Each certification evaluates different subjects and criteria.
Related article: JAS Organic: Your Complete Guide to Japan’s Organic Certification
Transparency Levels
Several restaurants do not fully disclose basic information such as price ranges, operating hours, and reservation methods on their official websites. This may reflect different information management policies or update frequencies, but it means you may need to contact restaurants directly before visiting.
Specific Percentages of Organic Ingredients
Most restaurants do not publish specific figures such as “organic ingredients account for 95% or more of total procurement.” Even restaurants holding JAS Organic Restaurant certification, which implies management according to certification standards, typically do not disclose exact percentages.
Environmental Practices vs. Health Claims
References to “sustainable practices” in this article primarily mean environmental considerations such as waste reduction and sustainable sourcing. Some restaurants’ independent philosophies emphasize “health commitments” (such as using ionized water), which may have limited scientific support and should be understood separately from environmental practices.
Making Your Choice
There is no single correct answer when choosing an organic restaurant in Tokyo.
Some people prioritize third-party certification. Others connect with farm-to-table business models. Some want buffet-style variety. Others seek restaurants specializing in specific areas such as seafood or vegan cuisine.
The information presented here serves as material for your decision. Consider which elements matter most to you right now and what kind of experience you’re looking for.
You don’t need to act immediately. Choosing not to visit any of these restaurants is also a valid decision. Your choice is respected.
If you’re interested in learning more about organic standards and sustainable food systems in Japan, exploring resources on organic certification processes and Japanese agricultural practices can provide helpful context for making informed dining choices.
