This thesis studies the design of agro-food processing chains using quantitative methods from the fields of Process Systems Engineering and Supply Chain Management. It presents an approach to optimise strategic decisions in the agro-food industry at the product level, the process and enterprise level, the supply chain level, and the network level. Case study results show that using non-conventional intermediate products and production processes can reduce the agro-food industrial energy and water use with respectively 22% and 37%, while reducing costs by 13%. Additionally, supply chain configurations were identified that allow for a reduction of the carbon footprint of over 30% without a reduction of the total gross margin. The decisions at the different levels are interdependent, and sequential optimisation of the different levels will lead to sub-optimisation of the agro-food processing chain. The approach presented in the study enables to reconsider the current set-up of agro-food processing chains and reduce inefficiencies in the production of food.