The apse chapels had almost all altars of carved or marble inlaid, serving some of them provisionally, for more than 400 years as sites of the tombs destined to the Pantheon of D. Duarte.

The cover of fine ribbed vaults is the work of master Huguet. It is in this monastery that the first stained glass windows are introduced, through masters from the Netherlands during the 15th century. In the century. XVI the stained glass windows in Portugal are already built by the Portuguese vine masters (António Taca pai and son 1530-1587) disciples of these foreign masters (Conrate 1428-66 Flamengo, Guilherme Beluy 1442-77 Flamengo, Luis Alemão 1438-59).