During his visit to Arequipa, Viceroy Francisco Toledo was informed by the Town Corporation about their wish, from years back, to found a monastery of nuns. He gave the necessary licenses to found the private monastery of nuns of the Order of Saint Catherine of Siena.

Several years later, Doña María de Guzmán, the widow of Diego Hernández de Mendoza, a beautiful young lady who had no children, decided to retire into the yet unfinished monastery, giving to it all her fortune. On the 10th. of September 1579, the Memorial and Capitulation of the foundation of the Monastery was signed by the Town Corporation, the Judiciary, the Regiment of the City and the Bishopric of Cusco. The Town Corporation delivered the four plots owned by the city for its functioning and appointed Doña María de Guzmán as "the first to live within and be prioress of said Monastery".

On Sunday 2nd. of October 1580 a high mass was celebrated in the city and Doña María was acknowledged as the founder and took the habits formally.

The ladies who entered as nuns were Creole, half-bred and even daughters of curacas (Indian chieftains). In 1964 the first Spanish nuns entered. History tells of the intake of poor nuns and from ladies of the city, who without embracing the religious life entered into the Monastery to exert their virtues.

In 1582, Arequipa suffered a severe earthquake and the Monastery was badly damaged. In spite of that, the retirement was kept. Then, a period of suffering started during which the nuns themselves repaired their rooms. Due to lack of money the chapel was not repaired and the "Holy Sacrament" was exposed in a hut made of straw.