The Academy has two separate institutions:
- The Under and Tuglas Literary Institute of the Estonian Academy of Sciences is a research and development institution that conducts interdisciplinary and innovative fundamental research on Estonian-language literature and the multilingual literature of the Estonian territory from the Middle Ages to the present day, placing it within the cultural context of the Baltic Sea region, Europe and the world.
- Estonian Academy Publishers issues seven international, peer-reviewed, open-access scientific journals that are indexed in leading international databases.