A place of profound sacredness, the crypt was chosen by Saint Charles Borromeo as a personal place of prayer, where he went every Wednesday and Friday afternoon. It was not uncommon to see him spend entire nights in what he himself defined as "the gym of the Holy Spirit", adoring the simulacrum of Christ's tomb. For this reason, after his canonization, a polychrome terracotta statue was placed depicting the saint kneeling in front of the sarcophagus. The crypt also allows visitors to come into contact with one of the oldest testimonies of the city's history. The flooring, made up of large slabs of white 'Verona' stone, in fact comes from the paving of the ancient Roman forum from the 4th century, the main square of the Roman civitas, where the major civil and religious activities took place.

Reopened to the public after fifty years in 2016, the crypt was subsequently the subject of a complex restoration project financed by MIBAC and completed in late spring 2019, mainly aimed at recovering the decorated surfaces.