I quite often pop in to Henderson's at St John's after my Saturday morning French class. It's an outpost of the original Henderson's on Hanover Street, which has been serving vegetarian food in Edinburgh since the 1960s. Note that one of the earlier reviews is actually describing that one, not this one.
Henderson's at St John's is in the undercroft of St John's Episcopal Church, which is well known for activism in social justice and human rights. The café is next door to the Peace and Justice Centre, a Christian bookshop and the One World Shop (temporarily relocated to Nicholson Square due to ongoing refurbishment work).
The cafe is really a vegetarian canteen, with all dishes on display and described in detail on a blackboard, coded for gluten-containing ingredients. On my latest visit, I had a bowl of celery, broccoli and leek soup (£4.25). I was asked if I wanted bread, which I did; I think oatcakes are also available. I was also given croutons (fried with black pepper and garlic, I think) on the side and some butter. If you don't want butter, you should say. Chilled tap water with mint and lemon is available on a side table; just help yourself.
The soup was old-school wholefood; the kind you can just about stand a spoon up in. The bread was good, tasty wholemeal; the croutons were made from the same bread. So, this place is nothing fancy but you'll get a filling lunch in a part of town where there aren't a lot of veggie options. It's great if you're shopping on Princes Street and need to refuel. You can also choose one of several hot dishes, served with your choice of a range of salads (just over a tenner).
Due to its location, this café does attract an older crowd. I had a lovely conversation with a spritely 87 year-old Dutch-Scottish lady who asked if she could sit at my table while she waited for her friend. Also worth noting that, whether you sit inside or out, you will be surrounded by funerary monuments! You will, though, get an atmospheric, historic setting to enjoy your lunch.
Cons: Fairly pricey; shabby toilets