The oldest portion of the complex is the open chapel, which dates from the time when the structure began as a small mission. The chapel is integrated into a "porteria" (a porch like entrance or arcade) in the front of the building, which was added in the 1560s. The altarpiece of the chapel is recessed into the back wall which has a pediment and contains ten panels. The central figure is of the Archangel Michael, the original patron saint of the mission. Above him is a female saint, possibly Saint Clare, with archangels and luminaries of the Church on the surrounding panels. God, the Father looks down from the pediment with the Four Evangelists at the base.