Overall, the church’s interior has maintained its medieval appearance. It has a longitudinal plan and decorated wooden beams on the ceiling, a possible reference to Noah’s Ark , the ark of salvation. The single chamber structure has excellent acoustic properties, enabling everyone to follow the prayers and listen to the sermons and precepts of the Christian doctrine.

A common trait of these churches is the square apse termination, covered by a cross vault whose starry sky decoration evokes the Creation. Inside is a wooden choir made in 1687: it is one of the characteristic features, important to Carmelite life as the friars would gather here to pray during the day and to take part in liturgical ceremonies. Two wooden doors, carved with the three theological virtues of Faith, Hope, and Charity and with the allegory of religion separate the choir from the nave where the faithful gathered. The step that runs along the walls of the nave was used either to access the side altars or the Chapel of the Holy Sacrament when the church was crowded or as a dividing element between the area for the congregation and the sacred area of the side altars, because it is important to remember that even these were reserved for Mass and prayers.

Of the many side altars erected in the church in past centuries, only three have survived to this day: one is located along the left wall, near . . .