My father-in-law lives very centrally and mostly shops at his nearest Hanamasa.

There was* a closer supermarket in the local shotengai shopping street but he stopped going there when friendly familiarity went over a threshold and liberties were being taken which made him uncomfortable. It’s more of a detached experience at the Hanamasa and he likes to keep it that way.

A lot of the 100 yen stores have a few staples that are typically cheaper than at a convenience store.

If we’re coming back from an excursion somewhere it’s nice to pick up local produce from that area, or else we might get something whilst making our way through a fresh produce section of a depachika as we head out of one of the main stations such as Shibuya.

I personally look out for farmers’ markets, they are all over Tokyo but you need to become aware of them. Depending on where you are based and where you are visiting there are a whole range of options at a whole range of price points. The hard part for people living alone is often the decision whether to buy food to make from scratch or whether to get it pre-prepared, often it’s a combination.
I personally find it much easier to shop for food in Tokyo now that I’m making meals for 4 of us than I did back many years ago when I stayed in my own lodging.

*I’m saying “was” as I have just discovered that this local supermarket has been torn down since my last visit in 2019