Inside Iglesia de San Francisco you'll find elaborate stone carvings and decadent altars. Visit the church’s Museo de Arte Religioso (Religious Art Museum) to see 17th-century religious paintings by indigenous artists. It also has the creepy catacombs – in one room you'll see the orderly tombs of monks, and in another are the skeletons recovered from indigenous graves found at the site, laying bare and without ceremony.
The intricately sculpted Capilla de la Dolorosa to the right of the nave is considered one of the finest chapels in the city.