He began his academic career at Central European University (Budapest), where in the 1990s he taught international relations and European studies. He subsequently held positions at the European Centre for Minority Issues in Belgrade and Sarajevo, working as a regional representative and ethnopolitics advisor(2001–2006). From 2006 to 2010 he taught at the University of Kent (UK), then moved to the University of Graz, where since 2010 he has been Professor of History and Politics of Southeast Europe and, since 2011, Director of the Centre for Southeast European Studies.
From 2019 to 2023, Bieber held a Jean Monnet Chair in the Europeanization of Southeast Europe. He has also been a visiting scholar and lecturer at Cornell University (USA), the London School of Economics (UK), New York University, and other leading universities.