On 4 November 1538 Ottavio married Margaret of Austria, the illegitimate daughter of Charles V, Holy Roman Emperor.

Pope Paul III attempted to regain Piacenza; he set aside Ottavio's claims to the succession of Parma,[citation needed] where he appointed a papal legate, giving him back Camerino in exchange, and then claimed Piacenza from the emperor — not for the Farnese, but for the Church.

During the interregnum that followed, Ottavio again tried to induce the governor of Parma to give up the city to him, but met with no better success; however, on the election of Giovanni Maria Ciocchi del Monte to the papacy as Julius III, the duchy was conferred on him in 1551.

Julius III, who was anxious to be on good terms with Charles V on account of the Council of Trent which was then sitting, ordered Farnese to hand Parma over to the papal authorities once more, and on his refusal hurled censures and admonitions at his head, and deprived him of his Roman fiefs, while Charles did the same with regard to those in Lombardy.

The rest of his life was spent quietly at home, where the moderation and wisdom of his rule won for him the affection of his people.