The Church of Our Lady of Mercy was intended to be an intermediate place between Mexico City and the missions established in the region that now corresponds to Guatemala. It was built in the early 17th century.

Due to several earthquakes, the original temple was demolished, and in 1646, the construction of a new temple began, which was completed in 1690 and dedicated to the Virgin of Mercy. Additionally, as part of the improvements, the convent was expanded to create one of the first schools in the region.

Due to the Reform Laws, the convent had to be abandoned, but the church remained in service. In 1898, Bishop Gillow acquired the property and started its renovation.

The church has a single nave, and its decorative elements date from different periods, as it has suffered damage from various earthquakes.