As Capelas Imperfeitas (The Unfinished Chapels) remain as a testimony of the fact that the monastery was never actually finished. They form a separate octagonal structure tacked on the choir of the church (via a retrochoir) and only accessible from the outside. It was commissioned in 1437 by King Duarte I as a second royal mausoleum for himself and his descendants. But he and his queen Leonor of Aragon are the only ones buried here. The original design, begun by Huguet, was altered by successive architects, especially Mateus Fernandes (who is buried inside the church). The octagonal rotunda has seven radiating hexagonal chapels. In the corners of the chapels stand the massive unfinished buttresses, that were intended to support the vault. These pillars, designed by Diogo Boitac, are decorated with Manueline motives carved in stone.
The portal rises to a monumental fifteen metres. It was originally built in Gothic style, but was transformed beyond recognition by Mateus Fernandes into a masterpiece of Manueline style (completed in 1509). It is completely decorated into a lacework of sumptuous and stylized Manueline motives : armillary, spheres, winged angels, ropes, circles, tree stumps, clover-shaped arches and florid projections. This homage of King Manuel I to his predecessor King D. Duarte mentions his motto Leauté faray tam yaserei (I will always be loyal). This motto is then repeated more than two hundred times in the arches, vaults and pillars of the chapels. Portal of the Unfinished Chapels.
The Renaissance loggia, added at about 1533, was probably meant for musicians. It is ascribed to the architect João de Castilho.