Details of his life are sparse. He was born in Alcáçovas, in Alentejo, southern Portugal. He is known to have been a choir boy at Évora where he subsequently studied with Manuel Mendes. His first position was as mestre de capela of the cathedral of Évora; sometime before 1589, he became maestro di cappella at the Hospital Real, Lisbon. By 1591 he was appointed as mestre de capela at the cathedral in Lisbon, a position he held till 1639. This was the most prestigious musical appointment in the country.
He also served as director of the Seminar of São Bartolomeu, and was also a professor of music at the 'Colégio do Claustro da Sé' (College at the Holy See Cloisters) in Lisbon, where he taught Manuel Machado.
While chronologically his life overlapped with the beginning of the Baroque music era, he was a rather conservative composer who followed the techniques of the Renaissance masters of the previous generation. Palestrina's polyphonic style played a crucial role in his compositions throughout his life.