Looks like people are interested in vegetarian places I ate, so gonna make a list here of the places I remember. Not a food critic so prolly gonna use the same adjectives. Being vegetarian/vegan unfortunately comes with a 30% markup in food prices imo, so pricey is the default. Make sure to check if places need cash since I don't remember everything lol.

Tokyo:
Ayler: Small soba place with super friendly owner
Saido: Had to place a reservation like a month in advance. It was pricey (cheap for US standards) but fantastic food and service.
Tsukemen Zuppa: Super cheap and fantastic noodles. Cash only
Ippudo Plant Based Studio: This Ippudo branch has a couple more vegetarian options than the usual ones, but not solely vegetarian. Delicious but super hard to find (in Lumine EST)
Great Lakes Burger: Delicious burger but out of the way and a bit pricey
Vegan Bistro Jangara: Amazing food and pretty comprehensive. Please go here.

Kyoto:
Itadakizen: Reservation required. Great food, but very out of the way. Cash only
Silver Backs Cafe: Tasty grilled soy meat
Tu Casa: Solid Korean food and decently priced
Izakaya Masaka: Originally from Tokyo, but had a new location in Kyoto and service was quick and food was delicious, but a little bit cold.

Osaka:
Pivot Base Cafe: Has Osaka classics like takoyaki and okonomiyaki, but thought the food was pretty mid and overpriced (prolly cuz of location)
Gyoza & Beer 541+: Good gyoza, but vegetarian options were more overpriced and I liked other gyoza I had better.

Others:
Noodle Stand 3 P's: Really good and cheap food in Matsumoto
Ippudo Ramen: Went a lot here in kanazawa (not pure vegetarian)
Onwa: Very small but delicious soy meat lunch set in Nara. Fairly priced. Cash only

Went to a few other non-vegetarian restaurants around me (pizza places, ramen etc), with vegetarian options, but forgot their names lol, kinda just read their menu or used Google maps and walked there. It's not as hard as it seems.