A place of deep sacredness, the crypt was chosen by Saint Charles Borromeo as his 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 called the gym of the Holy Spirit, in adoration of the simulacrum of Christ's tomb. For this reason, after his canonization, a polychrome terracotta statue depicting the saint kneeling in front of the sarcophagus was placed. 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, actually comes from the pavement of the ancient Roman forum of 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, subsequently the crypt underwent a complex restoration funded by the MIBAC and completed in late spring 2019, mainly aimed at recovering the decorated surfaces.