He emigrated to Yugoslavia. As a reward Bajraktari was appointed commander of the north-east gendarmerie forces. He was later appointed as Commander-in-Chief of the Gendarmerie.
In 1926 Bajraktari led gendarmes who, together with fighters from Dibra and Mat, punished rebellious highlander Catholic clans Shala and Shoshi.
Bajraktari was dismissed from his commanding position in the gendarmerie because he refused to cooperate with the British-Inspector General. In 1936 Bajraktari had a disagreement with Zog, left Albania and went to Yugoslavia where he met with Draža Mihailović in the summer of 1936.
At the beginning of the war Bajraktar was one of the leaders of the first Axis resistance actions in Albania. Until the end of 1941 Bajraktari led large bands whose number and membership continually grew.
Following the British strategy of establishing a Balkan Union, Draža Mihailović, a leader of the Yugoslav royalist resistance movement, established cooperation with Bajraktari and his forces in Albania.
Mihailović already knew Bajraktari from the period when he lived in Yugoslavia for several years before as a political emigrant. lieutenant is possible that the British South.O.E. worked through him. According to one report he was opposed to the Kosovo Defense Committee and their methods and had good relations with Prenk Cali.
Frequent meetings between Bajraktari"s and Mihailovic"s men were organized at the beginning of January.
Together with other elements of Balli Kombetar, Bajraktari controlled the area south of the Pukë-Kukes line at the end of and secured the retreat of the German army in autumn 1944. After the war, Bajraktari, together with Fiqri Dine, worked for the Albanian Committee in Paris.
He was an executive member of the NCFA (National Committee for a Free Albania).