A paleochristian church at the site, dedicated to the Holy Sepulcher (Santo Sepolcro) was located near here, and the first documentation of a monastery here date to 1090.

This church, which held his relics, was rebuilt starting about this time, and leading to consecration in 1236, with the bell-tower dating to 1237, and the facade to 1257.

Amadeo also designed and sculpted the elements of the Arca di San Lanfranco which serves as funereal monument and tomb to the saint.

During the Siege of Pavia in 1524, which ended in the Battle of 1525, the King of France Francis I established his headquarters in the monastery.

The choir, located along the side walls of the presbytery, consists of two bodies of nine stalls each, separated by perforated barriers, with cockpit seats and smooth back panels on the top framed by a lobed motif.

Among the most notable, is a fresco depicting the murder of St Thomas Becket, whose life had parallels with San Lanfranco.