Climate change, in combination with population growth, is placing increasing pressure on the world’s oceans and their resources. This is threatening sustainability and societal wellbeing. Responding to these complex and synergistic challenges requires holistic management arrangements. To this end, ecosystem-based management (EBM) promises much by recognising the need to manage the ecosystem in its entirety, including the human dimensions. However, operationalisation of EBM in the marine environment has been slow. One reason may be a lack of the inter-disciplinary science required to address complex social–ecological marine systems. In the present paper, we synthesise the collective experience of the authors to explore progress in integrating natural and social sciences in marine EBM research, illustrating actual and potential contributions. We identify informal barriers to and incentives for this type of research. We find that the integration of natural and social science has progressed at most stages of the marine EBM cycle; however, practitioners do not yet have the capacity to address all of the problems that have led to the call for inter-disciplinary research. In addition, we assess how we can support the next generation of researchers to undertake the effective inter-disciplinary research required to assist with operationalising marine EBM, particularly in a changing climate.