The church, started by Boitac, has a nave and aisles (three-aisled church with five bays) under a single vault (25 x 25 m), with slender, articulated columns and a projecting transept (29 x 27 m).

Established near Toledo in 1374, the Hieronymite Order soon became popular in Spain and Portugal, and in 1415 it numbered 25 houses. Prince Henry the Navigator (1394-1460) founded S Maria de Belém, a chapel of the Order of Christ, for mariners. Soon after his accession Manuel I (reigned 1495-1521) decided to build a grand monastery for the Hieronymite Order, which would continue to serve mariners as well as providing a burial place for the king. It also commemorated Vasco da Gama's successful return from India and was built with money from the spice trade; he is buried in the church. This project drained funds from the work at Batalha, which remained unfinished. The complex includes the church, monastery, sacristy, and refectory. It is a UNESCO World Heritage Site.