In the context of the Common Fisheries Policy Reform, the implementation of multiannual management plans for fisheries and the annual quota negotiations between EU member states has generated a growing demand from stakeholders and managers for integrated advice that goes beyond the usual biological advice. This has led to the emergence of bio-economic tools and methods for the comparison of the biological, economic and social tradeoffs associated with alternative options for fisheries management. A Decision Support Framework (DSF) has been developed in this context, with the objective to tackle technical and methodological challenges to be able to provide bio-economic advices to support decision at national and European level. It is based on a partnership approach involving the fishing industry, managers and scientists and on technical protocols. We present the development of a partnership DSF within three local case studies, highlighting key challenges and lessons learnt regarding appropriateness and application of a DSF. The data processing methods and collaborative platform were pivotal for scoping out objectives and management options, and for aligning DSF outcomes with decision makers' needs and agendas. Definition of common standards and institutionalization of the use of partnership DSF are still required to operationalize the integrated advice process at national and European levels.