Los Pyramides
The retreat has a great little veggie restaurant open to non-guests.
Moonfish
Excellent mostly vegi fare for breakfast, lunch and dinner. chai tea, the best, house-roasted coffee in the world, brownies made with their own cacao, sandwiches for 25-30q including grilled tofu or falafel, pizzas, salads from their garden, and more.
Aaculaax
Serves a good breafkast from 8am-10am daily, on a balcony overlooking the garden and the lake.
On the way from the dock to the square, there is a small fruit shop on the left, with fruit on display near the curb. Inside, a a lady makes tasty sandwiches for 10Q, and sometimes other simple foods. It's one of the cheapest options in San Marcos. They don't always have food - you'll have to drop by and see.
San Marcos is known for its vegetarian cuisine. The open air markets provide great, fresh produce for very cheap so if your interested you are able to find an array of ingredients to cook a home cooked meal.
Moonfish Cafe has the best fresh fruit pancakes I have ever eaten in my life. Not to mention they were huge and delicious and only cost us 10 Q!
The street food is also very delicious and I never seemed to have a problem with my stomach after eating it. The locals take full advantage of the local produce so majority of the offered dishes are vegetarian and all are fresh!
Allula is a Japanese sushi bar. I found it very interesting that there is Japanese food even in Guatemala. From my experience, all of the sushi seemed very fresh and had a Guatemalan twist to it for sure!