This church suffered extensive damage in the 1650 earthquake and had to be completely demolished. Around 1631, in addition to the church, portals were built on the square under the rectorship of the priest Luis Ferrer de Ayala. The church was considered one of the beautiful and imposing in Peru and became the largest that Society of Jesus had in the viceroyalty. This first church had a Plateresque-style façade and the main altarpiece was begun by Bernardo Bitti. Likewise, near Intik'ijllu street, they built the Chapel of Nuestra Señora de Loreto destined for the Indians. On July 17, 1571, the Colegio de la Transfiguración del Señor and the Church of la Compañía de Jesús, were founded, beginning that same year the construction of the first building that served as a church. The price of the property amounted to 12,000 pesos and was paid based on donations made by Teresa Orgóñez, daughter of Rodrigo Orgóñez - lieutenant of Diego de Almagro - and her husband Diego de Silva y Guzmán. Once in Cusco, Viceroy Toledo authorized the Jesuits to occupy Amarucancha, which then belonged to the heirs of Hernando Pizarro. They arrived at the imperial city on January 12, 1571, before the viceroy who delayed attending to government issues of the country.

The road to Cusco was made by the Provincial Father Jerónimo Ruíz de Portilla accompanied by Luis López, Antonio Gonzáles Ocampo and three more priests who left Lima together with Viceroy Francisco de Toledo. The Jesuits arrived in Peru on March 29, 1568, landing at the port of El Callao and entered Lima on April 1.

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