The complex underwent significant improvements in 1685, but it was in 1759 when the Spanish architect Juan Manuel Villagómez modified the temple again, adding the beautiful baroque main altar and two side altars. During the Reform era, it was severely damaged, and the complex was divided.

Inside, there is a sculpture dedicated to the Lord of Forgiveness, believed to be of Guatemalan origin, as well as an image of Our Lady of Mount Carmel from the 16th century, placed in the main niche of the presbytery altarpiece.

In the 19th century, the baroque altarpieces were replaced by neoclassical-style quarry stone altars. The main altar stands out with its magnificent image of Our Lady of Mount Carmel and two murals painted in the early 20th century by Candelario Rivas, a painter from Zacatecas.

During the latest restoration, the original 18th-century tiles were recovered from the domes and the tower.