The internal structure has three naves. In the right aisle of the first altar is the statue of San Gaspare del Bufalo, the Roman Saint founder of the Congrega del Precziosissimo Sangue. A large canvas in the church iconographically recalls a miracle that occurred through the saint's intercession.
In the left aisle there are the altar and the statue of Saint Stephen patron of Putignano, dated 1691. The city strongly wanted both the altar and the statue as a sign of gratitude and devotion for the liberation from the plague in 1656.
Continuing further, still in the left aisle, in a niche, there is the precious reliquary of Saint Stephen containing a fragment of the saint's skull.
In the central nave dominates the high altar, dated 1745, made of inlaid polychrome marble, which harmonizes well with the upper altar, that of the oratory (1746 - 1747), the latter accessible thanks to two stone stairs placed at the sides of the main altar. In the central part of the oratory, the high altar, there is the icon of Maria SS la Greca or of the Madia.
The choir preserves the remains of the presbytery of the primitive church, in it you can see four columns that support a ribbed vault.
In the vault, above the imposing pillars, a circular dome rises, which from the outside is manifested by an octagonal extrados.
Inside the church there are statues depicting St. Peter, St. Paul, St. Catherine and another unidentified saint, as well as part of a frieze, which presumably depicts the Annunciation. These works were all made by the artist Stefano da Putignano.