At the death of his father, he was first at Tagliacozzo under Ascanio Colonna, and then to Città di Castello where he was introduced to the military career by his uncle Alessandro Vitelli.
In 1550 he was on a frigate in a Christian fleet led by Carlo Sforza, to fight against the northern African raider Dragut.
[1] 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.
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.