The Viceroy Francisco Toledo, during his visit to Arequipa, was informed by the council of canons of their wish to found a convent. In response, the viceroy granted them the necessary licenses for the founding of the "Monasterio de Monjas Privado de la Orden de Santa Catalina de Siena," or “Private Convent of the Sisters of the Order of Saint Catherine of Siena.” Years later, Doña María de Guzmán, the widow of Diego Hernández de Mendoza—a beautiful, rich, young woman who never had children—decided to shut herself away in the convent, which was still under construction, and give away all her earthly belongings. On September 10, 1579, the record and agreement for the founding of the convent was signed between the City Council, the Chief Justice, and the Regidor’s Office of Arequipa and the Bishopric of Cuzco. After signing the document, four plots of city-owned land were ceded for the site of the convent, and Doña María de Guzmán was named "first inhabitant and prioress of said Convent.”
On Sunday, October 2, 1580, a high mass was held in the city and Doña María, recognized as the founder, formally donned her habit.
The women who entered the convent as nuns included women of mixed race, European descent, and even the daughters of indigenous curacas, or chiefs. It was not until 1964 that the first Spanish nuns joined. History also tells us of "poor nuns" and ladies from Arequipa’s high society, who—without giving their life over fully to religion—came to the convent for a time to practice their virtues.
In 1582, Arequipa suffered a major earthquake that seriously damaged the convent’s building. Despite this, the cloister remained standing. The event marked the start of a period of hardship, however, in which the nuns themselves were forced to repair their own rooms. Due to a lack of money, the chapel could not be renovated, “for which reason the Most Blessed Sacrament was put on display in a straw hut.”