Located just beneath the presbytery of the church, this space is of immense aesthetic and architectural value and is one of the best-preserved areas among the ancient convents of New Spain. Here, the friars and their benefactors were buried, which explains its luxurious decoration, also based on tile work and mural painting. The coat of arms of Sargento Mayor Juan de Ortega y Valdivia shows that he was the owner of the most luxurious chamber. This space was restored in 1990. The small central altarpiece is, along with the one in the domestic chapel, the only original one that has survived. It frames the 17th-century painting "The Lord of the Column", which inspired Villalpando in one of his sacristy paintings. Miraculously, it remains in place, as there are photographic records of works of art that once decorated this space but have since disappeared. With mannerist influences, the painting is attributed by Manuel Toussaint to Baltasar de Echave Orio, one of the pillars of Novohispanic art. It was here, in 1916, that Zapatista troops excavated in search of legendary treasures; to their surprise, they only found twelve mummified corpses due to the nature of the underground.

The discovery of the mummies was a major event in the community, to the point that when a friar tried to bury them, he faced strong opposition from the locals who had already adopted them as part of their community.