Daigo 醍醐 (Minato-ku)
Daigo is actually a 2-star Michelin restaurant so you will be left completely speechless by the presentation and taste of these incredible dishes. There are different "Kaiseki" (Japanese course where each dish is served one after the other) courses to choose from. They start at ¥10,000 for lunch; for dinner, they start at ¥15,000.
Sougo 宗胡 (Roppongi)
Sougo is interesting for its combination of traditional shojin cuisine in a modern decor. The quality is really good, yet the prices are still fairly reasonable. You can get a lunch set for just ¥1,500, but if you're looking for something more luxurious, they also serve some high-end lunch courses for ¥5,000. For dinner, the courses are between ¥6,000 to ¥10,000.
The restaurant also has cafe hours from 14:00 to 17:00 during which you can order a la carte various light meals and desserts for about ¥600 to ¥1,000.
Bon 梵 (Taito-ku)
Bon serves a kind of Shojin cuisine called Fucha that was introduced to Japan by Chinese monks some 300 years ago. The presentation is incredibly beautiful and they use only the best seasonal ingredients to prepare the many dishes. It's a bit on the expensive side, with Fucha lunch courses that start at ¥5,000 (¥3,500 for the simple lunch box), and dinner courses from ¥6,000 to ¥10,000, but it is well-worth the go! You'll enjoy not just the meal but also the beautiful traditional atmosphere of the restaurant.
Kamakura Fushikian 鎌倉不識庵 (Akihabara)
This vegan cafe is located in Akihabara - not exactly the kind of place you'd expect to find Buddhist cuisine! The best thing about this place is that it's actually quite cheap with shojin plates that are just ¥980 to ¥1,530 for lunch.
You might want to try their Japanese-style sweets too! The ice cream is also vegan.
Tera Cafe 寺カフェ (Daikanyama)
"Tera Cafe" literally means temple cafe, and as the name implies, it's actually a temple of sorts where there are monks that come in to give consultation at certain times. They also serve some Buddhist cuisine for about ¥1,000 to ¥2,000. The idea behind the cafe was to make a place where you can walk in casually, enjoy healthy cuisine and have peaceful conversations. The interior is essentially modern and feels like a fashionable Tokyo cafe but with some Buddhist decorations.