In the church of the Santo Domingo Convent, as in many Christian churches, there are typically four crypts: one in the Main Altar (in the case of Santo Domingo, it has two sections), two in the Transept (one on each side), and another in the Narthex. In turn, the church floor plan is divided into three sectors: the Epistle Aisle, the Central Aisle, and the Gospel Aisle.

In the Church of Santo Domingo, in addition to the four crypts mentioned above, there is a fifth crypt, the same one that Anselm Pi Rambla, Francesc Serrat and the then Prior entered in 1982, located in the Nave of the Epistle.

After extensive research, we believe that its precise location in this sector was not accidental and serves an important role in the Koricancha for several reasons.
The first reason is that it is located next to the Solar Hall (the most important hall of the Inca Empire). The second reason is that it connects to the Chinkana, which links to all the underground tunnels of Cusco. The third, and no less important reason, is that after much investigation, we firmly believe that this crypt contains the remains of Tupac Amaru I, Sayri Tupac, his wife and sister Cusi Guarcay (three children of Manco Inca, grandchildren of Huayna Capac), and their daughter, Doña Beatriz Clara Coya.

The deduction we make that this royal Inca family is buried in this fifth crypt is thanks to the excellent research conducted by María del Carmen Martín Rubio, a Ph.D. in American History from the Complutense University of Madrid and a collaborator with the Spanish National Research Council; the Peruvian historian and jurist Ella Dunbar Temple (1918–1998), Countess of Primeglio; and important documents studied at the National Library of Peru.

Tupac Amaru I, the legitimate son of Manco Inca, married Guasua Chumbi and had two children: a son, Don Martín, and a daughter, Doña Isabel. In 1571, upon the death of his brother Tito Cusi Yupanqui, Tupac Amaru I (or Topa Amaro, as written in the 16th and 17th centuries) assumed the throne and consequently found himself compelled to continue the struggle against the Spanish from the kingdom of Vilcabamba, the center of Inca resistance and political power established by Manco Inca.

These events coincided with the appointment of the new Viceroy, Francisco de Toledo, who was given very strict orders to end the kingdom of Vilcabamba upon his arrival in Peru. On June 24, 1572, the capital of Vilcabamba la Grande fell, and Tupac Amaru, along with some of his generals, was captured by Captain Martín Oñaz de Loyola. The victorious army and its prisoners entered Cusco on September 21, and preparations for the trial, sentencing, and execution of the Inca began swiftly, with Tupac Amaru being imprisoned in the fortress of Colcampata.

On October 1, 1572 (María del Carmen Martín Rubio, Buscando a un Inca: La Cripta de Topa Amaro, 2005:80), he was beheaded in Cusco's Plaza de Armas by Viceroy Francisco de Toledo. This event caused immense sorrow among the Peruvian population, as they witnessed the extinction of their dynastic lineage. The execution also provoked shock in Spain and Europe, leaving Viceroy Toledo's reputation significantly damaged.

According to a deed granted on August 16, 1592, by the Provincial and Prior of Santo Domingo to Doña Beatriz Clara Coya, daughter of Sayri Túpac and Cusi Guarcay, a patronage and a vault in the main chapel of the church of the Santo Domingo Convent were sold to her in perpetuity. Beatriz financed the construction of this crypt on her own, building it over the foundations of the Temple of the Sun. In exchange, she ceded to the Dominican fathers an estate in the valley, which included an orchard, a mill, and a textile workshop (Betancurt y Túpac Amaro, 1790: T. III, 120).

In 1600, the ñusta Beatriz Clara Coya formalized a will in which she declared herself a resident of Cusco and named her daughter, Doña Ana María de Loyola Coya, as her legitimate heir. In the will, she ordered that upon her death, she be buried in the Santo Domingo Convent in Lima and that her remains later be transferred to the burial site in the Dominican convent in Cusco, which was her property and where the remains of her parents and relatives already rested (Betancurt y Túpac Amaro, 1790: T. III, 156v).

In 1780, in an official document drafted by Vicente José García Rodríguez, representative of Don Felipe Betancurt y Túpac Amaru, to establish his genealogical tree, it is noted that the tomb of the last Inca of Vilcabamba, Tupac Amaru I, was intact at that time in the Santo Domingo Convent. Several prominent individuals from Cusco testified, including the city's perpetual alderman, that the crypt had been opened on that occasion to view the remains of the Inca. The document contains key phrases such as: "...the vault of the main chapel was opened..." and "...entering from the epistle aisle on the right-hand side..." (Martín Rubio, Buscando a un Inca: La Cripta de Topa Amaro, 2005:92).

In the course of our excavation work conducted in the Santo Domingo church, we have no doubt about the accuracy of the statements in these documents. The reference in (Betancurt y Túpac Amaro, 1790: T. III, 120), which states: "she financed the construction of this crypt on her own over the foundations of the Temple of the Sun," and the other document specifying: "entering from the epistle aisle on the right-hand side," clearly indicate the location of the fifth crypt identified during our work. This area is currently sealed off by the Dominican Order.