Most of the church was built between 1490 and 1495, and in 1496 the nuns of Order of Poor Clares were already living in the monastery. After 1495, under Manuel I, the nave of the church was covered with stone vaulting, replacing the wooden ceiling originally planned. It is believed that, in the 1510s, King Manuel I ordered the apse of the church to be rebuilt, although this is contested by some authorities. Founder Justa Rodrigues Pereira and her family were buried in the crypt of the church, located in the main chapel.