It was built between the sixteenth and eighteenth centuries in the so-called Andean Baroque style. Milestones in its history include:

In 1548, the Convent of San Francisco was founded along the Choqueyapu River by Fray Francisco de Morales. In August 1549 the construction of the first Church of San Francisco began, which was concluded in 1581. Between 1608 and 1612 the first church collapsed as a result of a snowfall of considerable proportions. Between 1743 and 1744 the construction of the present church began. In 1753, the closure and the roof of the church's dome were completed. On April 23, 1758, it was consecrated. In 1790, the carved façade is finished. In 1885, the construction of its single tower began. In 1948, it was declared a minor basilica. Between 1950 and 1960, part of the convent was demolished. Since 1965, the church houses a museum.