The crypt, located below the main altar, is very large and can be considered a subterranean church in its own right. It is decorated with marble sculptures by Francisco Leopoldo e Silva depicting the history of Job and St Jerome.
The crypt has the tombs of all bishops and archbishops of São Paulo. Of special note are the bronze tombs of two important historical figures: Father Diogo Feijó and the cacique Tibiriçá. Feijó was regent of Brazil during the infancy of Emperor Pedro II. Tibiriçá was the cacique (chieftain) of the Guaianás tribe who, in the 16th century, welcomed the first Jesuits to the Piratininga Plateau and whose aid made the foundation of São Paulo possible.
In 2004, the human remains of Bartolomeu de Gusmão (1685–1724), a Jesuit from the former Portuguese colony of Brazil and innovator of lighter-than-air airship design, were transferred to the crypt.