In 1570, when a war between Venice and the Ottoman Empire was upcoming, he revised the fortifications of Cerines and Famagusta, of which Baglioni became governor, in collaboration with the city's rector Marcantonio Bragadin. In the same year the island was invaded by the Turks. Baglioni launched several counterattacks but was finally forced with his troops in the walls of Famagusta. After the fall of Nicosia, the Turks laid siege to Famagusta, and Baglioni launched a series of successful raids against the besiegers. The Turks lost some 52,000 men in five major assaults until, in late July, the Venetians, despairing to receive any rescue from the homeland, decided to surrender. The Turk commander, Lala Kara Mustafa Pasha, accorded the survivors to safely return to Crete, but he did not keep his word: Bragadin, Baglioni and other Venetian commanders were imprisoned, beaten and beheaded.