The design of agri-food systems is a major concern for society and public health. Crises such as COVID-19, the war in Ukraine and climate change are causing upheaval and prompting transition and innovation to ensure the resilience of these systems. Their complexity requires a holistic approach to guarantee their overall performance and sustainability. Design is the process of creating new systems, and is considered a crucial stage in innovation. We have set ourselves the objective of developing an original approach by testing the methods and tools of Industrial Engineering in the agri-food field on the one hand, and applying this approach to a food supply chain on the case of pineapples on the other. Process modeling, FMEA and continuous flow simulation were tested. They proved to be feasible and relevant for enriching commonly used methods.