Chain-cafe-operator Pronto is, remarkably, the manager of this stylish all-day cafe in a visitors centre added to the compound of Tsukiji Hongwan-ji in 2018. The set meals are great value, in particular the set Japanese breakfast with 18 different items. If you're just after a snack, it also does a good range of teas and cakes.
Cafe Tsumugi
Ginza & Tsukiji