The World Food Programme (WFP) is the largest humanitarian agency fighting hunger worldwide, reaching approximately 90 million people with food assistance across 80 countries each year. To deal with the operational complexities inherent in its mandate, WFP has been developing tools to assist its decision makers with integrating supply chain decisions across departments and functional areas. This paper describes a mixed integer linear programming model that simultaneously optimizes the food basket to be delivered, the sourcing plan, the delivery plan, and the transfer modality of a long-term recovery operation for each month in a predefined time horizon. By connecting traditional supply chain elements to nutritional objectives, we are able to make significant breakthroughs in the operational excellence of WFP’s most complex operations. We show three examples of how the optimization model is used to support operations: (1) to reduce the operational costs in Iraq by 12% without compromising the nutritional value supplied, (2) to manage the scaling-up of the Yemen operation from three to six million beneficiaries, and (3) to identify sourcing strategies during the El Niño drought of 2016.