With Ivane Javakhishvili’s support, Berdzenishvili began research at the Department of History at Tbilisi University. Berdzenishvili became professor in 1939, and over the next two decades he taught at Tbilisi University, Kutaisi Pedagogical Institute, and Tbilisi Pedagogical Institute and worked at the State Museum and Georgian Academy of Sciences. In 1941-1965, he directed history and historical geography courses at Javakhishvili Institute of History. In 1944, he became a member of the Academy of Sciences, and in 1946-1956, he directed the History Department at Tbilisi University. In 1951-1957, he was vice-president of the Georgian Academy of Sciences. Berdzenishvili established himself as a preeminent authority in the field of the history of Georgia, and he produced pioneering works on various aspects of history, among them the nine-volume Sakartvelos istoriis sakitkhebi.
Niko Berdzenishvili died in 1965.