The 1582–83 census registered that the vilayet, an autonomous part of the frontier of the Sanjak of Scutari, had the nahiyah of Grbavci (13 villages), Župa (11 villages), Malonšići (7 villages), Pješivci (14 villages), Cetinje (16 villages), Rijeka (31 villages), Crmnica (11 villages), Paštrovići (36 villages) and Grbalj (9 villages); a total of 148 villages.

The Montenegrin tribes, with support of the Serbian Orthodox Eparchy of Cetinje, fought guerilla wars against the Ottomans with some degree of success. Although the Ottomans continued to nominally rule the country, the mountains were said to have never been completely conquered. There existed tribal assemblies (zbor). The head bishop (and tribal leaders) often allied themselves with the Republic of Venice. The Montenegrins fought and won two important battles at Lješkopolje, in 1604 and 1613, under the leadership and command of Metropolitan Rufim Njeguš. This was the first battle, of many, that a bishop had led, and managed to defeat the Ottomans.

During the Great Turkish War, in 1685, Suleiman, Pasha of Scutari, led a contingent that approached Cetinje, and on the way clashed with hajduks in Venetian service under the command of Bajo Pivljanin at the hill of Vrtijeljka (in the Battle of Vrtijeljka), where they annihilated the hajduks. Afterwards, the victorious Ottomans paraded with 500 severed heads through Cetinje, and also attacked the Cetinje monastery and the palace of Ivan Crnojević. The Montenegrins expelled the Ottomans and asserted independence after the Great Turkish War (1683–1699).