When he was fourteen, he succeeded his father as organist in 1718 and two years later moved to Lisbon, where he gave harpsichord lessons and met Domenico Scarlatti, who lived in Portugal, from 1721 to 1728. It is claimed that when the king’s son, Dom António, arranged for Scarlatti to give Seixas harpsichord lessons, Scarlatti replied that it was Seixas who should give him lessons. Seixas later became organist in the court chapel and Lisbon cathedral as well as court composer. He was knighted in 1738 by John V of Portugal.
Much of his work was destroyed in the earthquake which devastated Lisbon in 1755. Only three orchestral pieces and around 100 keyboard sonatas survive, plus a handful of choral works for liturgical use (much more conservative than what one would expect from his instrumental music).
Macario Santiago Kastner published collections of the sonatas in Portugaliae Musica.