Over my time in Ecuador I came back to Cuenca several times and love to share some of my favorite spots with you!
I stayed in different places and I can recommend two main ones, this hostel Hostal Yakumama (for social and shared) and a hotel I stayed in called La Posada del Rey, which was amazing due to the lovely ladies here. I also stayed at Guillerminas Hostel Boutique but this was a little bit intense smell and not much privacy, Mallki Hostel 2 which was great but a bit far out of the center and Airbnb Pedrito which I do not recommend due to cold water, noise and wanting to extra charge us.
For food and places to eat, going close to the university area is perfect. Here you have very affordable menu del dias, also veggie lentil soups.
Other spots to eat:
EFÁ Clásico bakery (the best bread in town)
Nandala Cocina Vegetariana
C41 Coffee Lab
Pura Vida Cuenca
El Nuevo Paraíso (veggie restaurant with a menu del dia for 3 dollars)
YúA Restaurante
Morlacos Tacos Sucursal
Punjabi Rasoi Indian Restaurant
Shopping groceries at Supermaxi and Mercado 10 de Agosto is perfect. Here you can also get a limpia, a spiritual cleansing. Buy tabacco and other beautiful things. The Plaza de las Flores has a lady in the corner who also sells tabacco and agua de florida. Lots of stores on this square sell fajas for protection too. Gracie’s Naturals is a cute store which sells a lot of nice products, creme for the body, organic tooth paste and much more!
I recommend to take a day trip to Las Cajas, you can go to the bus station and find a bus that goes there. Hike around and enjoy.