The Compañía de Jesús (Jesuits) was one of the first religious congregations established in Oaxaca, and soon extended its evangelizing efforts to the people of the Zapotec and Mixtec regions, where some of the priests even preached in the local languages.
Arriving in Oaxaca in 1576, the group founded the Colegio Seminario de San Juan, located next to the church of Nuestra Señora de Las Nieves, and later opened other learning centers. Around 1579, work began on the construction of their own church and convent in the center of town, west of the Casas Reales. The congregation moved their location to the Casas Reales in 1596 because of jurisdictional problems with the Dominicans, even though the temple was not finished.
The Convento y Templo de la Compañía were turned over to the bishop of Oaxaca in the late 18th century, during the expulsion of the Jesuits, and were occupied by the Sisters of the Conception. Part of the former convent was to be sold and later used for commercial purposes. The Convent and Church were declared a historical monument in 1933, and in 1950 the Jesuits once again began to manage the temple.