Throughout the clerestory windows are not large. They are round-headed of two lights, with simple tracery, and deep splays both inside and out. The large transept windows with half octagonal heads under a large trefoil were inserted about the beginning of the sixteenth century.
Inside the resemblance to Batalha is less noticeable. The ribs of the chancel vault are well moulded, as are the arches of the lantern, but in the nave, which cannot have been finished till the end of the fifteenth century, the design is quite different. The piers are all a hollow square set diagonally with a large round shaft at each corner. In the aisle arches the hollows of the diagonal sides are carried round without capitals, with which the round shafts alone are provided; while the shaft in front runs up to a round Manoelino capital with octagonal abacus from which springs the vaulting at a level higher than the sills of the clerestory windows.[83] The most unusual part of the nave is the vaulting of all three aisles, where all the ribs, diagonal as well as transverse, are of exactly the same section and size as is the round shaft from which they spring, even the wall rib being of the same shape though a little smaller. At the crossing there are triple shafts on each side, those of the nave being twisted, which is another Manoelino feature. The nave then must be about a hundred years later than the eastern parts of the church, where the capitals are rather long and are carved with foliage and have square abaci, while those of the nave are all of the time of King João II. or of King Manoel. At about the same time some small and picturesque windows were inserted above the smaller apses on the east side of the transept, and rather later was built the chapel to the north-east of the nave, which is entered through a segmental arch whose jambs and head are well carved with early renaissance foliage and figures, and which contains the simple tomb of a bishop. The pulpits, organs, and stalls, both in the chancel and in the western choir gallery, are fantastic and late, but the great reredos which rises in three divisions to the springing of the vault is the largest and one of the finest in the country, but belonging as it does to a totally different period and school must be left for another chapter.