This high altar was commissioned by Queen Catarina (Catherine of Austria), the wife of João III, in 1571. The high altar was designed by the master builder Jerónimo de Ruão in a Mannerist style, a total contrast to the Manueline body of the Church.
Found in open arches, between pairs of lateral columns, and held by marble elephants are the tombs of Manuel I and his Queen Maria, on the left side (the Gospel side) and João III and Queen Catarina on the right hand side (the Epistle side). Behind the high altar, is a retable with paintings depicting scenes from the Passion of Christ and the Adoration of the Magi by the artist Lourenço de Salzedo (1572-1574).
The silver Tabernacle is the work of the Portuguese goldsmith João de Sousa (1674-1678). This Tabernacle was a gift from Afonso VI in thanksgiving for victory at the Battle of Montes Claros in 1665 which restored Portugal’s independence.