The agro-food industry is one of the largest parts of the European Union’s economy and faces economic and environmental stresses. While food traceability systems (FTSs) inform supply chain actors of product and logistical attributes, large scale implementations are scarce and are do not support active decision making. We present a framework developed for FUTUREMED project used to perform a data-driven analysis that considers both micro and macro aspects of a food supply chain (FSC). With its comprehensive multiple-depth data architecture incorporated within a tailored decision-support platform, this framework and the resulting decision-support tool is the first to move beyond simple traceability implementation to the sustainable planning of food logistics, bridging the gap between research techniques and real-world data availability. We define KPIs that measure a subset of economic and environmental factors to quantify the impact of logistical decisions. We validate the framework with the case study of an Italian fruit trader that is considering opening a new warehouse. We conclude by suggesting that this framework be applied to more complex case studies and be enhanced through including more dimensions of sustainability.