In this paper we assess the level and modalities of stakeholder engagement in the 38 EU-funded FP6 biodiversity research projects and the impacts of doing research in a more participatory way on policy, society and science. We look both at impacts on the ‘research users’ as well as on the ‘producers’ of research outcomes. In particular, we explore how and when scientists make use of stakeholders’ input in the research process. To fully capture the complexity of the interactions we first develop a new typology of stakeholders and the roles they play. Our data indicate that half of the projects engaged mainly during the dissemination stage and not at critical stages of problem definition and methods selection. When fruitful interactions between science and society occur during the whole research process this often results in the foundation of innovative research programmes and transdisciplinary networks clustering around particular topics. This produces improved assessment of environmental change and effective policy proposals. We conclude that the complexity of the issues around biodiversity governance and the failure to halt biodiversity loss in Europe calls for more holistic and inclusive procedures of knowledge production at the science–society interface.