Since 2007, the Institute for Southeast European Studies has been a cooperation partner in the Research Centre for Eastern and South Eastern Europe in Regensburg and an affiliated Institute of the University of Regensburg. Its employees collaborate in southeastern European research in various institutions and committees at national and international level. Particular highlights are the lively partnership and exchange relationships which the institute library has with local institutions, in Germany and with around 200 libraries in southeastern Europe and throughout the world.

The Institute is also a member of the following associations:

• Arbeitsgemeinschaft der Bibliotheken und Dokumentationsstellen der Ost-, Ostmittel- und Südosteuropaforschung e.V. (ABDOS)

• Arbeitsgemeinschaft der Spezialbibliotheken (ASpB)

• Arbeitsgemeinschaft historischer Forschungseinrichtungen in der Bundesrepublik Deutschland e.V. (AHF)

• Arbeitskreis für Siebenbürgische Landeskunde e.V. (AKSL)