King Philip I appointed him Rector of the University of Coimbra and, later, Bishop of Faro; he later resigned to take up the post of Inquisitor General of Portugal.

Fernão Martins de Mascarenhas was born in Montemor-o-Novo, Alentejo, the second-born of D. Vasco Mascarenhas, Keeper of the Wardrobe (Reposteiro-mor) of Prince John (son of King John III), and Maria de Mendonça.

During his episcopate, the Algarve endured a plague outbreak, and Bishop Mascarenhas assisted the sick with great commitment; when Vila Nova de Portimão faced a terrible famine, he had all the wheat in his granary distributed amongst the populace.

In 1599, he established the Jesuit College in Portimão and, in 1607, he donated large sums to help build the Capuchin Convent of Saint Anthony in Tavira.

[3] He accumulated this post with that of Councilor of State, and of Lord Prior of the Collegiate Church of Our Lady of the Olive Tree [pt] in Guimarães.