Located in the south wing is the church, which follows the late medieval tradition of monastic churches. It has a quadrangular floor plan with a single nave and chapels set between original butresses; it does not have a transept and it adheres to the traditional typology and features of the Valencian Gothic. It has a deep presbytery and an extensive choir at the foot of the temple. It has two access ways. The first leads to the exterior and its soberly constructed Gothic door, based on mouldings and pilasters, following the typical moulded ogival style, opens onto the plaza. Over the door can be seen a stand, which used to house an image of the Virgin Mary, now disappeared. The second door provides access to the cloister.
The primitive 14th Century church was in Gothic style, with five ogival diaphragm arches that divided it into sections; it had a gabled roof. During the 18th Century the church was transformed into the Gothic style; to achieve this part of the arches were demolished in order to increase their height and to cover the nave with a barrel vault with lunettes. The Chapel to the Virgin of Health, constructed in the 18th Century, used to stand on the Epistle side, but the only part of this that remains is the door that bears the anagram of the image of the Virgin. Ausias March chose the side chapels as the burial tombs for his two wives, Isabel Martorell and Joana Escorna.
A feature of the altar area of the church is a wide rectangular chancel from which two access ways open, one on each side, which lead to two small rooms that flank the tabernacle. This area has a quadrangular floor plan and is covered by a cupola with a lantern and baroque decoration with plant motifs. The floors is covered with Valencian tiles from the 16th Century.
The choir is located at the foot of the church and its lower part is divided up into two sections, one of which is delimited by two round arches. Between these can be found a groin vault, which is flanked by two more arches that are also rounded and frame the entrances to the church. These arches are supported by capitals bearing the coat of arms of the first Duke of Gandia, Alfonso I of Aragon, decorated with figurative, plant and pastoral motifs.
The upper choir has a rectangular floor plan and is covered by a stellar vault with lunettes, which were decorated with paintings and venerations in the corners. The roundels that are distributed around the vault are also decorated.