Bonwetsch joined the History Department at University of Hamburg in 1972.
From 1973 to 1980 he was assistant professor at the Department of East European History and Geography of the University of Tübingen.
Bonwetsch taught from 1980 to 2003 as a professor of Eastern European history at the University of Bochum.
In 2000 he received an honorary doctorate from the Kemerovo State University and in 2004, he received from the Karasin National University Kharkiv another honorary doctorate.
In 2003, he was the founding director of the German Historical Institute Moscow.