As the environmental issues facing our planet change, scientific efforts need to inform the sustainable management of marine resources by adopting a socio-ecological systems approach. Taking the symposium on “Understanding marine socio-ecological systems: including the human dimension in Integrated Ecosystem Assessments (MSEAS)” as an opportunity we organized a workshop to foster the dialogue between early and advanced-career researchers and explore the conceptual and methodological challenges marine socio-ecological systems research faces. The discussions focused on: a) interdisciplinary research teams versus interdisciplinary scientists; b) idealism versus pragmatism on dealing with data and conceptual gaps; c) publishing interdisciplinary research. Another major discussion point was the speed at which governance regimes and institutional structures are changing and the role of researchers in keeping up with it. Irrespective of generation, training or nationality, all participants agreed on the need for multi-method approaches that encompass different social, political, ecological and institutional settings, account for complexity and communicate uncertainties. A shift is needed in the questions the marine socio-ecological scientific community addresses, which could happen by drawing on lessons learnt and experiences gained. These require in turn a change in education and training, accompanied by a change in research and educational infrastructures.