In the reign of D. Manuel, the monastery is reformed.

Bishop D. Vaz Vaz Gavião who would have accompanied D. Manuel to Santiago de Compostela in 1502 is named prior to the monastery, and begins the renovation campaign. Jacques Boytac who works in Portugal (Jerónimos, Torre de Belém, Convento de Jesus de Setúbal) since 1492 is the master, and organizes the new church with a single nave with vertical volume that connects with the side chapels.

Between 1518-22 the Manueline cloister is finished, now under the orders of the master Marcos Pires, Boytac is "Master of the Works of the Kingdom" and leaves for Arzila where he tries to redo the defenses of that North African fort. D. Manuel intends to exalt the first Kings of Portugal, moving the tombs from the old cloister to the main chapel, in two very high quality tombs, designed by Nicolau Chanterene and Diogo de Castilho, and sculpted by the same team that worked on the Jerónimos portals. , is also the work of the same team of artists. The beauty of this facade lies in the solution of using the clear tone of the Stone of Ançã for the axial Portal, highlighting it and highlighting it in contrast to the yellow tone of the limestone facade of the area of Bordalo.

At the initiative of Prior D. Pedro Gavião, in 1507 the reformulation of the Romanico building began. Boytac is the master, and organizes the new church with a single nave with vertical volume that connects with the side chapels. The current reconstruction allows the visitor to see some of the structures of the old Romanesque monastery.

The shape of the old Romanesque church appears to have been 3 naves. They preserved the arches and pillars between the central nave and the lateral nave on the wall of the current area of ​​the nartex, under the high choir.