Underneath the major altar there is the crypt, which has a cruciform layout, dated back to the X century (the Byzantine period) and decorated with frescoes of various ages. On the walls you can see fragments of frescoes from the 13th and 14th centuries, which once decorated the entire room. Particularly significant is a paltry triptych depicting San Cataldo, Maddalena and St. Zosimus that gives communion to Santa Maria Egiziaca. In fact, the triptych consists of three images dating back to different periods.

San Cataldo, was an Irish Christian monk of the seventh century, who landed in Taranto to carry out his work of evangelization in the pagan city and he became the bishop there. His arrival is combined with several miraculous phenomena that the Saint did for the city. In 1071 the remains of San Cataldo were discovered in the Baptistery belonging to the Cathedral during the renovation of the city after the disasters of the Saracen war. They found a marble sarcophagus, inside in perfect condition there was the body of the Saint also recognized by the opistograph cross found on the chest of the Saint with the name Cataldus. From that moment, San Cataldo became the patron saint of Taranto.

Leaning against the eastern wall you can see a sarcophagus from the end of the 13th century, on which a bas-relief depicts a deceased (probably a girl) in the ascent, supported by two angels. In the crypt room there are the tombs of some archbishops of Taranto.