Some new residents of Kyoto ask this to me.
Unfortunately there are not many good (means good variety and good deal) supermarkets in Kyoto-city. I guess because there is not enough space to built since Kyoto is the old city, and FRxxCO, the most famous supermarket in Kyoto, which is pretty expensive and they don’t have good variety nor quality, are everywhere like a monopoly.
So my answer is… Takashimaya!
Takashimaya is a posh department store which is located in downtown, so my young friends believe that their grocery section is expensive. Actually it’s not!
For example I found Japanese broccoli for 100yen which was 230yen in the FxxSCO in the same day. Also petit tomatoes were 290yen which were 100yen cheaper than the FRExxO. See?!
Takashimaya is proud of their quality and service so their fruit and vegetable are also really good!
In addition, their bicycle parking is free for 3 hours if you buy something.
So I park my bike then I just buy my favorite 198yen ciabatta bread of Peck, the cool Italian bakery that they have in underground, and walking around downtown for 3 hours!
This is a tip for new residents of Kyoto!