The interior consists of a basilica with three naves, while the apse is the result of the extension attributed to Giovanni Pisano. To the left of the entrance, under a fourteenth-century triptych with the enthroned Madonna with Child and Saints, visitors can see a Roman sarcophagus dating to the third century. To the left is the large baptismal font, divided in two sections: the square basin with the Deesis (the Christ adored by the Virgin Mary and St John the Baptist) and the stories of San Cerbone and San Regolo.
At the centre of the counter façade, the rose window is embellished with rare fourteenth-century glass. In the last chapel on the right the Crucifix painted by Segna di Bonaventura stands out (dated to the beginning of the fourteenth century). On the altar by Flaminio Del Turco (1626) is the wooden multi-coloured crucifix, which replaced the one by Giovanni Pisano, now in the Museum of Sacred Art.
Behind the altar, at the centre of the choir, is the coffer of San Cerbone by Goro di Gregorio (1324). It is shaped as an urn, displaying eight stories of the saint’s life in the lower section.
The Maestà, attributed to Duccio di Buoninsegna (1316), is situated in the last chapel on the left. Just below the presbyteral area is the crypt, within which are arranged eleven small statues of prophets and saints.