From 1564 to 1565, he was Bishop of Sabina and it is conjectured (in the absence of positive evidence) that it was in 1564 that Farnese finally was consecrated a bishop. He was certainly a bishop when he was the principal Consecrator of Cardinal Giulio della Rovere on April 15, 1566. From 1565 to 1578, he was Bishop of Tusculum (Frascati). He was the Bishop of Porto from 9 July 1578 to 5 December 1580. He was then Cardinal-Bishop of Ostia and Velletri and Dean of the College of Cardinals from 5 December 1580 until his death on 2 March 1589.