Seixas was born in Coimbra. He succeeded his father as organist in 1718 at age fourteen, and two years later moved to Lisbon, where he gave harpsichord lessons and met Domenico Scarlatti, who was living 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 the king João V.
Seixas was influenced by the German Empfindsamer Stil (literally 'sensitive style'), but he also added his own portuguese style. Much of his work was destroyed in the earthquake that devastated Lisbon in 1755. Only three orchestral pieces and around 100 keyboard sonatas survived, plus a handful of choral works for liturgical use (much more conservative than what one would expect from his instrumental music).