The Jesuits arrived in Peru on March 29, 1568, landing at the port of El Callao and entered Lima on April 1.

Once in Cusco, Viceroy Toledo authorized the Jesuits to occupy Amarucancha, which then belonged to the heirs of Hernando Pizarro.

Likewise, near Intik'ijllu street, they built the Chapel of Nuestra Señora de Loreto destined for the Indians.

Around 1631, in addition to the church, portals were built on the square under the rectorship of the priest Luis Ferrer de Ayala.

The new project contemplated a larger church than the one demolished with two lateral chapels, three doors on the square and a bell of 100 quintals.

The order requested permission from the Viceroy García Sarmiento de Sotomayor for the use of the Pucyura quarry, which was granted on September 16, 1653.

The construction of the new church faced opposition because the plans were considered daring and would diminish dignity and importance to the Cathedral with which it kept very little distance.

The written opposition was formulated by the bachelor Diego Arias de la Cerda on October 22, 1656, before the viceroy, who issued a ruling favorable to the Jesuits.

This decision was appealed by the Bishop of Cusco Pedro de Ortega y Sotomayor before the Real Audiencia while the construction of the church continued.

The solemn transfer of images and relics and collation of the new church of la Compañía de Jesús, whose title is the Transfiguration of the Lord, was celebrated with the feast of the glorious Saint Ignatius of Loyola, Tuesday, July 31 of 1668, in which the venerable dean and Cabildo made the offices, and Dr. Don Eugenio Gómez de la Vaquera, canon of this church, said the panegyric prayer, with the assistance of the Cabildo, clergy and religions, being rector of said school Father Juan of Urquiza".The church remained under the power of the Jesuit Order until the expulsion ordered by King Charles III of Spain.

The last third corresponds to the bell tower that has: The lower part of the facade has a large door with a wide opening that culminates in a segmental arch.

From the internal ends of the cornices, the lateral entablatures follow a semicircular arch cut in its central and upper portion.

It has Solomonic columns, a large number of paintings, a central canvas representing the Transfiguration of Jesus, a sculpture of the Virgin of the Immaculate Conception, and various ornaments and decorations made with precious stones that highlight the Baroque style of the complex.

Similar sumptuousness is seen in the carved tribunes and the rest of the altarpieces, some of which belonged to the defunct Templo de San Agustín.

The church exhibits, under the choir of the main altar, works of art by Marcos Zapata and his assistant Cipriano Gutiérrez.

That building originally served the Universidad San Ignacio de Loyola, which was part of the University of the Transfiguration, created by Pope Gregory XV in 1621.

[13] After the Jesuits were expelled in 1767, the site served as the army barracks and prison of José Gabriel Condorcanqui (Túpac Amaru II).

The chapel is small and austere, with a single nave built in stone, and has a more sober portal than that of the main church.