Improvement in nutrient recycling in agriculture is essential to maintain food production while minimising nutrient pollution of the environment. For this purpose, understanding and modelling nutrient cycles in food and related agro-industrial systems is a crucial task. Although nutrient management has been addressed at the plot and farm scales for many years now in the agricultural sciences, there is a need to upscale these approaches to capture the additional drivers of nutrient cycles that may occur at the local, i.e. district, scale. Industrial ecology principles provide sound bases to analyse nutrient cycling in complex systems. However, since agro-food social-ecological systems have specific ecological and social dimensions, we argue that a new field, referred to as “Agro-Industrial Ecology”, is needed to study these systems. In this paper, we review the literature on nutrient cycling in complex social-ecological systems that can provide a basis for Agro-Industrial Ecology. We identify and describe three major approaches: Environmental Assessment tools, Stock and Flow Analysis methods and Agent-based models. We then discuss their advantages and drawbacks for assessing and modelling nutrient cycles in agro-food systems in terms of their purpose and scope, object representation and time-spatial dynamics. We finally argue that combining stock-flow methods with both agent-based models and environmental impact assessment tools is a promising way to analyse the role of economic agents on nutrient flows and losses and to explore scenarios that better close the nutrient cycles at the local scale.Read less <