He was consecrated Archbishop of Goa in 1595, when he was only 35. As Archbishop of Goa, Menezes focused on strengthening Catholic ascendancy in Portugal. In 1612 Aleixo de Menezes was appointed Archbishop of Braga, Portugal.
He was viceroy of Portugal during the Philippine Dynasty from 1612 to 1615.
He died in 1617, his remains are located at the Populo Church in Braga, Northern Portugal. The result of his Synod of Diamper was unfortunate.
The Catholic Encyclopedia (1913) says:.