Reorienting food systems towards improving nutrition outcomes is vital if the global goal of ending all forms of malnutrition is to be achieved. Crucial to transitioning to nutrition-sensitive agriculture is valuing and measuring nutritional quality of the outputs of agricultural production. We review existing indicators which capture an element of nutritional quality applicable to different stages of the food and nutrition system. Applying relevant indicators from the agricultural production stage to selected aquaculture systems, we compare and contrast their strengths and limitations. 'Nutritional yields', 'potential nutrient adequacy' and 'Raos quadratic entropy' show particular promise in capturing the ability of a production system to nourish the most people and could be useful tools for prioritising investments and decision-making in the public, non-government and private sectors driving agriculture."