Food guide

Being a vegetarian and speaking no Japanese, I thought it would be a bit of a nightmare trying to find things to eat in Japan. Luckily I was (mostly) wrong, and the food turned out to be some of the best I've ever eaten. Plenty of places have English menus and there are a lot of healthy/organic cafes that have the best range of vegetarian options. There are also a lot of good quality Italian restauarants, and several Indian and Nepalese curry houses - both of which are a good bet for veggies. Eating out is not particularly expensive; especially good value are 'set' lunch and dinners which usually offer lots of small dishes for a fixed price. All of the places listed below are veggie-friendly and have English menu/staff.

Tokyo

Potluck (lunch, sandwiches)
A great lunch spot in Shibuya (in the basement of Opening Ceremony), it serves Vietnamese ban minh (baguette sandwiches stuffed with meat, egg, or veggies).
Potluck website

Cafe Ratia (healthy, fusion)
Tasty east/west fusion food in a minimalist-designed restaurant behind Harajuku's main bustle (near the Ukiyo-e Museum). We ate deep-fried tofu and chicken, balsamic glazed veggies, and bruschetta.
Cafe Ratia website

Japanese Vegetable Kitchen (healthy)
A fantastic find in Kichijoji, at the crossroads under the railway bridge near the park - look for the sign leading up a flight of stairs. Not all veggie but lots of options, food comes with bowls of rice, pickles and miso, with free roobois tea.

Sansar (Nepalese, curry)
Delicious curries served by friendly Nepalese staff, on a Shinjuku backstreet. Good value set thali-style meals. I'd walk back to Tokyo for more of their heavenly naan bread.
Sansar on bento.com

Gonpachi (teppanyaki)
Fantastic place housed in a converted warehouse in Roppongi, which apparently inspired the restaurant scene from 'Kill Bill'. Large menu of small tapas-style dishes, including chargrilled skewers of meat and veggies, fresh noodles, and amazing rice cooked in a hot stone pot. Upstairs is a more refined sushi restaurant. Slightly expensive but worth it for the experience.
Gonpachi website

Fonda De La Madrugada (Mexican)
Surprisingly authentic Mexican food in a large basement restaurant in Harajuku. Fun atmosphere with a live table-side mariachi band. Great cocktails and frijoles, rather expensive.
Fonda De La Madrugada website

Chibo (okonomiyaki)
Classy okonomikayi restaurant in Ebisu, in the Yebisu Garden Place complex. Great views and fun cook-it-yourself with the table hotplate.
Chibo website

Court Lodge (Sri Lankan, curry)
A small Sri Lankan eatery tucked into Shinjuku's business district to the west of the station. Unusual, authentic-tasting curries, and they also make their own range of sauces and chutneys which you can buy to take away.
Court Lodge website

Aureole (healthy, lunch)
A nice lunch spot facing onto Shinjuku Gyoen Gardens. Fixed price around ¥1000 (£6) for a starter salad, main, and cake for dessert. Mains include wholewheat pizza and California rolls.
Aureole website

Crayon House (healthy, organic)
Cafe/restaurant in Harajuku with its own health food shop attached. Food is alright, a bit bland. Lots of veggie options, nice ambience with lots of children and Japanese-stye sunken seating.
Crayon House website

Kyoto

Nishiki Market (ramen)
I don't even know the name of this place as it was in Japanese, but look for the red lanterns and kitschy 60s advertising posters on Nishiki Market. Great steamy little place with good booze and extensive menu. Big bowls of tasty ramen, and the fried sweet potatoes with sweetened butter dipping sauce are absolutely heavenly.

Cafe Rocka (vegetarian)
Basement cafe on the Ninenzaka near Kiyomizudera Temple, behind a cool design-y store. Tasty veg food including curry and teriyaki tofu wraps.

Kyodofu Fujino (tofu, vegetarian)
Tofu and yuba (tofu skins) done every way imaginable and all delicious (all vegetarian). On the 11th floor of the Isetan mall above Kyoto station - it doesn't get much more Japanese than a restaurant within a mall within a station. Set meals and a la carte; we shared a ¥3000 set meal between us which was about enough.
Kyodofu Fujino website

Kairas (oragnic, vegetarian)
A charming cosy little cafe that feels like it's converted from someone's home. The food is mostly vegan with a large menu (cutely hand-written and illustrated) including a good value set lunch. Fantastic food, great organic coffee, and a friendly owner. On the same road as the Kyoto Handicraft Centre.
Kairas on Happycow website

Kerala (Indian)
Old-skool British curry house styling on Kawaramachi Street. Nice menu with a large veggie section, good value.
Kerala on Bento.com

The Kitchen Salvatore Cuomo (Italian)
A classy Italian place on the 11th floor of Kyoto station Isetan. Nice views of the city from the window-side tables and really good, refined Italian food. Dishes are fairly small and designed to be shared. Pretty pricey.
Salvatore Cuomo website

Mikoan (vegetarian)
Extremely special place which went to on our last night in Japan. A tiny bar with about ten seats, packed to the rafters with books and trinkets and a whole family of live-in tabby cats (they had newborn kittens when we visited, so adorable). The owner cooks everything on a tiny stove behind the bar and her mother helps out. ¥1000 (£6) gets you a whole tray full of little dishes including deep-fried yuba, tofu-filled spring rolls, sesame seaweed, hot ginger and chilli beansprouts and miso broth. If two of you order, you get different dishes so you can share. An amazing experience of high-end shojin ryori (Zen Buddhist vegetarian food) without the usual high price tag.
Mikaon on deepkyoto.com