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The shifting policy focus towards Ecosystem Based Management in Fisheries (EBFM) requires the integration of knowledge and disciplines and the engagement of stakeholders to support decision-making processes. Scientists contribute to this through (i) participatory research projects, (ii) stakeholder partnerships and (iii) institutional scientific advice processes. Understanding the role of scientists in such processes, the nature of the interactions between scientists, stakeholders and managers in knowledge integration and the link between science and policy is an emerging field of research addressing transdisciplinary challenges. In 2018, Ifremer-UMR AMURE organized the workshop ‘Science, Partnership and Decision-support in Fisheries’ bringing together international scientists from natural and social sciences to conduct a review based on twenty concrete case studies. Findings indicate that science-stakeholder-manager partnerships for decision-support in fisheries can play an essential role in the transition to EBFM. To foster this transition, eight recommendations are presented that cover the roles of the different participants, the expectations of partnerships, capacity building, the integration of the social sciences, and funding structures. Further, it is recommended that future research and innovation framework programmes into sustainable fisheries and other ocean uses should explicitly include mechanisms to foster transdisciplinary approaches and the development of best practices. Building-up networks and developing reflexive approaches to review experiences and practices for transdisciplinary approaches in EFBM decision-support will contribute to design the next generation transdisciplinary platforms and generating actionable knowledge towards EBFM.