In the same year he was raised to the office of chancellor of Scotland, and was appointed protonotary apostolic and legate a latere by the pope.
Before this he had been sent by Archbishop Affre to Rome, and had been appointed Roman prelate and protonotary apostolic. For thirty years he remained a notable figure in France, doing his utmost to arouse his countrymen from religious indifference.
He entered the Celestine order and came into prominence during the pontificate of his uncle, Gregory XII., by whom he was appointed bishop of Siena, papal treasurer, protonotary, cardinal-priest of St Marco e St Clemente, and later cardinal-priest of Sta Maria in Trastevere.
In 1567 he became one of the secretaries of state, receiving also about the same time the lucrative appointment of protonotary of Sicily, and in 1573 the death of Ruy Gomez himself made room for Perez's promotion to be head of the " despacho universal," or private bureau, from which Philip attempted to govern by assiduous correspondence the affairs of his vast dominions.
At the age of twenty-five he held several rich livings, had been notary and protonotary to the Curia, and was first secretary to the pope, in which capacity he conducted the correspondence with the nuncios (among them Pier Paolo Bergerio in Germany) and a host of other duties.