Agri-food production systems are major drivers of global sustainability challenges including climate change, freshwater scarcity, micronutrient deficiencies, and cardiovascular disease. There is an urgent need for more robust methods (e.g., life cycle assessment, system-based modelling) and metrics (e.g., Disability-Adjusted Life Years, nutrient diversity indicators) to quantitatively assess the sustainability of these production systems on a joint nutritional, health, and environmental basis. Creating a sustainable future will require actors to co-develop and co-implement interventions across these groups; presently, however, these fields are misaligned. Current methods are siloed, qualitative, and calorie- or food- based, and they should be developed in a more holistic, quantitative, and nutritionally-focused manner. Developing data-driven and interdisciplinary approaches can help to alleviate food security and sustainability challenges.