This paper describes some of the changes in the framework of terrestrial ecosystem research in the European Union. The major outcomes of the Terrestrial Ecosystems Research Initiative are presented, especially the lessons from the evaluation of the use of continental-scale transects in ecosystem research. The priority themes for future ecosystem research in view of the changing perception of scientific relevance for policy-making and society are presented. The barriers in the involvement of science end-users in the definition of research priorities and questions are also analysed.