Sustainability assessment of food supply chains is relevant for global sustainable development. A framework is proposed for analysing fishfood (fish products for direct human consumption) supply chains with local or international scopes. It combines a material flow model (including an ecosystem dimension) of the supply chains, calculation of sustainability indicators (environmental, socio-economic, nutritional), and finally multi-criteria comparison of alternative supply chains (e.g. fates of landed fish) and future exploitation scenarios. The Peruvian anchoveta fishery is the starting point for various local and global supply chains, especially via reduction of anchoveta into fishmeal and oil, used worldwide as a key input in livestock and fish feeds. The Peruvian anchoveta supply chains are described, and the proposed methodology is used to model them. Three scenarios were explored: status quo of fish exploitation (Scenario 1), increase in anchoveta landings for food (Scenario 2), and radical decrease in total anchoveta landings to allow other fish stocks to prosper (Scenario 3). It was found that Scenario 2 provided the best balance of sustainability improvements among the three scenarios, but further refinement of the assessment is recommended. In the long term, the best opportunities for improving the environmental and socio-economic performance of Peruvian fisheries are related to sustainability-improving management and policy changes affecting the reduction industry. Our approach provides the tools and quantitative results to identify these best improvement opportunities.