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The building has a basilica-style structure with three naves and a continual transcept ending in three apses of simple Benedictine design. The transcept consists of an enormous tripartite chamber with two transverse arcades showing the cross and connected by arches on top of which a cupola should rise but was never built. The gallery originally designed for women, however, is of Nordic derivation, the first of its kind to appear in Puglia. The inside of the Basilica is made especially attractive by the numerous supporting capitals, designed as truncated pyramids and decorated on all four sides. These are reminiscent of Byzantine designs, enlivened by figurative decorations and capitals in the shape of washbowls which bear motifs and forms of classical matrix with other markings of Anglo-Norman miniatures.

Beneath the internal transcept is the crypt, composed of thirty six bays covered with cross-shaped vaults supported on capitals - some of which are unadorned, Byzantine or late Medieval although most date back to the 11th century – with various decorative motifs, both anonymous and figurative. In the presbytery, a stone altar preserves the relics and has, for centuries, oozed manna; a liquid still distribted in ampollas to the devout. The entire holy building is paved with an opus sectile mosaic in Byzantine style with geometric motifs.

The outside of the structure has a solid, compact appearance with apses enclosed within a masonry curtain. The façade is flanked by two towers connected to the wings of the transcept by a continual series of great arches. The decoration of the portals stands out, as does the vestibule set on columns supported by stone griffins.

The building we see today is the fruit of a series of restoration campaigns between 1928 and 1956. The monumental carved wood and gold ceiling bears witness to the Baroque phase, with paintings by Carlo Rosa depicting Scenes from the life and miracles of the Saint.