This paper presents an analysis of a research project conducted by a network of environmental research institutes called Partnership for European Environmental Research (PEER). Our analysis constitutes a reflection on this research project based on a proposed ideal-typical transdisciplinary research process developed by Lang et al. (2012). The aim of the PRESS project (PEER Research on EcoSystem Services) was to provide support for the development and implementation of the EU Biodiversity Strategy to 2020, with a special emphasis on the ecosystem services concept. Our analysis of the research phases of the PRESS project shows that not all of the project elements accord with the notion of a full-scale transdisciplinary process. Despite this, a number of lessons can be learned regarding the use of different boundary objects for knowledge integration and the various roles played by researchers. We also identify some constraints with regard to synchronizing policy and project cycles and consider the advantages and disadvantages of research network structures in facilitating long-term cooperation.