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The application of global indices of nutrition and food sustainability in public health and the improvement of product profiles has facilitated effective actions that increase food security. In the research reported here we develop index measurements further so that they can be applied to food categories and be used by food processors and manufacturers for specific food supply chains. This research considers how they can be used to assess the sustainability of supply chain operations by stimulating more incisive food loss and waste reduction planning. The research demonstrates how an index driven approach focussed on improving both nutritional delivery and reducing food waste will result in improved food security and sustainability. Nutritional improvements are focussed on protein supply and reduction of food waste on supply chain losses and the methods are tested using the food systems of Kenya and India where the current research is being deployed. Innovative practices will emerge when nutritional improvement and waste reduction actions demonstrate market success, and this will result in the co-development of food manufacturing infrastructure and innovation programmes. The use of established indices of sustainability and security enable comparisons that encourage knowledge transfer and the establishment of cross-functional indices that quantify national food nutrition, security and sustainability. The research presented in this initial study is focussed on applying these indices to specific food supply chains for food processors and manufacturers.