In the conventual church, the cloister leaning against the church “where, on the ground floor, opened the rooms where the other acts of common life took place, the chapter house or room for solemn meetings of instruction and correction and government , attended by the friars of all times, because the room was also a cemetery, the refectory, with the facilities of its servant, and sometimes the library; upstairs, all around, the dormitories ran, with individual cells for study and rest; around the building, a cloistered field for space and size ". This Mannerist style cloister is composed of two floors, with a perfect archway between buttresses, in the first, and Ionic colonnade, in the second. Mateus Lopes, when crossing this cloister , it will have been inspired by the one of São João de Poio, in Pontevedra, in Galicia, made a few years before by him.

Four wings with vaulted edges, each profiling five perfectly round arches, two by two, on a continuous pedestal, with the central one remaining as an opening, guided by thick pillars that advance in front of the archival arch; the ornamentation, from the Ionic stylized on the pillars to the keys or pendants of the closing of the edges of the vault, to the corbels that close the archway, as well as to the four Mannerist masks that crown these in the angles of the square