He was apparently considered by his master Manuel Mendes as his favourite student; the latter left his own manuscripts to Magalhães, in the hope that these would be eventually published.
In 1589 Magalhães replaced Manuel Mendes as mestre do Claustro da Sé.
On the 27th of March 1623 he was appointed Mestre da Capela Real, a position he held until 1641.
He also wrote a book of plainsong, Cantus Ecclesiasticus, which was published in five different editions (the first ones in Lisbon in 1614 and in Antwerp in 1642, and the last one in 1724).
The catalogue of the Music Library of King John IV of Portugal also mentions one 8-voice Mass, 6-voice Lamentations for Maundy Thursday, one 7-voice Christmas villancico and five 5- and 6-voice motets.