Food and nutrition security is a persisting global issue and, in addition, food systems are now facing a new set of intersecting economic, social and environmental challenges. Recurrent socio-economic and biophysical changes put the sustainability of food systems at risk. There is an urgent need to develop knowledge-based tools to assess and monitor food sustainability and to identify pathways for food security and resource conservation. The systemic nature of these interactions calls for multidimensional approaches and integrated assessments for decision-making to guide change. This paper reviews social–ecological system frameworks with the view to conceptualize the sustainability issues that affect the food systems. It is argued that the understanding of the food systems as social–ecological systems, and inputs from the theories of vulnerability and resilience in particular, can provide the concepts necessary to understand and model the complex system dynamics involved in the multiple interactions between human and natural components.