There has been increased recognition of the importance of stakeholder engagement in the design, conduct and dissemination of research in support of Ecosystem-Based Management (EBM) of marine social-ecological systems. The complexity of such stakeholder engagement increases with the diversification of sectors, concerns and jurisdictions that must be accounted for, as development of the blue economy accelerates, particularly in coastal areas. Marine Protected Areas (MPAs sensu lato, including e.g. Marine Parks, Multiple Use Management Areas, Special Management Areas for certain maritime activities, …) constitute opportunities to establish integrated governance arrangements that bring multiple stakeholders together, in arenas which may support the long-term co-construction of policy-relevant research programs. They seem to offer a perfect test of the “living lab” concept which is on the rise. The aim of the workshop was to review and confront past experiences (both successes and failures) with respect to the co-design of EBM research in MPAs, and identify future needs and opportunities for the development of such research. Our guiding questions were: What knowledge is relevant to supporting MPA management? Considering disciplinary perspectives, observation methods, data, models, local knowledge, etc. What are effective collaboration approaches to integrate research and management in day-to-day operations of MPAs? How can we best deal with diverging expectations? How can we track the impacts of collaborative approaches and outcomes?