[1] Still a layman, he was proposed by the government of the Republic of Venice as Latin Archbishop of Nicosia, capital of the island of Cyprus.

The appointment by Pope Pius IV followed on 13 March 1560,[3] He received the pallium on 26 April and he was consecrated bishop in Rome on 1 May 1560 by Cardinal Gianbernardino Scotti.

After the end of the Council, Filippo went to Rome where he collaborated with the Holy Office,[1] and where on 19 May 1564 he was also appointed as General Commissioner of the Inquisition in Cyprus.

On 21 April 1566 the Council of Ten, to keep harmony with the local population, ordered him to maintain the existing ecclesiastical order, to postpone the publication of the decrees of the Council of Trent in the Orthodox rite churches and not to inform the Roman Curia of the disputes with the local Orthodox clergy.

[1] The process of his appointment as coadjutor of Aquileia was blocked by the discovery of a complaint against him, more than ten years earlier, by the inquisitor of Pera with whom Filippo had traveled to Trento.

Filippo was accused of possessing a forbidden book, the Ptolomey’s Geography commented by the Lutheran Sebastian Münster, and of having verbally supported the need to reopen in the council the discussion on the relationship between faith and works, a central point in the debate with the Protestants.

Thanks to the Venetian ambassador in Rome, Paolo Tiepolo, Filippo managed to avoid a formal trial before the Inquisition, but he had to renounce every new episcopal appointment, since a suspicion of heresy was enough to make one unfit for the care of souls.

[6] Then he moved to the camaldolese hermitage located on Monte Rua not far from Padua, where he died on 18 June 1586, as indicated in his gravestone once present in the local chapel of Santa Maria Assunta.

[7] Filippo Mocenigo published in 1581 in Venice a prominent treatise of Aristotelian philosophy, Universales institutiones ad hominum perfectionem quatenus industria parari potest, written with the intent of educating young people to defend the Catholic religion, with particular reference to the young people attending the German, English, Hungarian, Greek and Maronite colleges of Rome.