Reconciling food security, economic development and biodiversity conservation is a key challenge, especially in the face of the demographic transition characterizing many countries in the world. Fisheries and marine ecosystems constitute a difficult application of this bio-economic challenge. Many experts and scientists advocate an ecosystem approach to manage marine socio-ecosystems for their sustainability and resilience. However, the ways by which to operationalize ecosystem-based fisheries management (EBFM) remain poorly specified. We propose a specific methodological framework--viability modelling--to do so. We show how viability modelling can be applied using four contrasted case-studies: two small-scale fisheries in South America and Pacific and two larger-scale fisheries in Europe and Australia.