Food systems must become more sustainable and equitable, a transformation which requires the transdisciplinary co-production of knowledge. We present a framework of food sustainability that was co-created by academic and non-academic actors and comprises five dimensions: food security, right to food, environmental performance, poverty and inequality, and social-ecological resilience. For each dimension, an interdisciplinary research team—together with actors from different food systems—defined key indicators and empirically applied them to six case studies in Kenya and Bolivia. Food sustainability scores were analysed for the food systems as a whole, for the five dimensions, and for food system activities. We then identified the indicators with the greatest influence on sustainability scores. While all food systems displayed strengths and weaknesses, local and agroecological food systems scored comparatively highly across all dimensions. Agro-industrial food systems scored lowest in environmental performance and food security, while their resilience scores were medium to high. The lowest-scoring dimensions were right to food, poverty and inequality, with particularly low scores obtained for the indicators women’s access to land and credit, agrobiodiversity, local food traditions, social protection, and remedies for violations of the right to food. This qualifies them as key levers for policy interventions towards food sustainability.