BioScene (scenarios for reconciling biodiversity conservation with declining agriculture use in mountain areas in Europe) was a three-year project (2002-2005) funded by the European Union's Fifth Framework Programme, and aimed to investigate the implications of agricultural restructuring and decline for biodiversity conservation in the mountain areas of Europe. The research took a case study approach to the analysis of the biodiversity processes and outcomes of different scenarios of agri-environmental change in six countries (France, Greece, Norway, Slovakia, Switzerland, and the United Kingdom) covering the major biogeographical regions of Europe. The project was coordinated by Imperial College London, and each study area had a multidisciplinary team including ecologists and social and economic experts, which sought a comprehensive understanding of the drivers for change and their implications for sustainability.A key component was the sustainability assessment (SA) of the alternative scenarios. This article discusses the development and application of the SA methodology developed for BioScene. While the methodology was objectives-led, it was also strongly grounded in baseline ecological and socio-economic data. This article also describes the engagement of stakeholder panels in each study area and the use of causal chain analysis for understanding the likely implications for land use and biodiversity of strategic drivers of change under alternative scenarios for agriculture and rural policy and for biodiversity management. Finally, this article draws conclusions for the application of SA more widely, its use with scenarios, and the benefits of stakeholder engagement in the SA process.