The square cloister of the monastery measures more than 180 feet on each side.
The groin vaults are characterized by wide arches and windows with tracery resting on delicate mullions. Each wing consists of six bays with tracery vaults. The four inner bays rest on massive buttresses, forming broad arcades. The corner bays are linked by a diagonal arched construction and show the richly decorated corner pillars. The inside walls of the cloister have a wealth of Manueline motifs with nautical elements, in addition to European, Moorish and Eastern motifs. The round arches and the horizontal structure are clearly in line with the Renaissance style, while at the same time there is also a relationship with Spanish architecture. The decorations on the outer walls of the inner courtyard were made in Plateresco style; the arcades include traceried arches that give the construction a filigree aspect.
The construction of such a cloister was a novelty at the time.
The cloister had a religious function as well as a representative function by its decorative ornamentation and the dynastic symbolic motives, such as the armillarium, coat-of-arms, and the cross from the Order of Christ, showing the growing world power of Portugal.