Mathematical modeling of complex problems, with particular attention to multi-criteria and optimization models, is particularly effective for analyzing critical issues in the agri-food supply chain. These tools allow analyzing problems of different nature through the use of qualitative and quantitative criteria, often conflicting with each other, and decision alternatives. Their versatility allows adapting solid theoretical constructs to different contexts and application areas, ensuring a modeling that takes into account the peculiarities of the problem under examination. In fact, multi-criteria analysis tools and optimization models allow supporting decision makers in the different phases that characterize the agri-food supply chain. This work addresses in particular the decision problem related to the transition of agri-food products from the storage to the marketing phase, using the Analytic Hierarchy Process (AHP) method. Once the products have undergone transformation processes, they are stored in one or more warehouses for distribution to commercial activities. There are several choices to be made in this phase, including the choice of the commercial establishments in which to distribute the products. In particular, the use of the AHP method is proposed for the analysis of a decision problem relating to the choice of the warehouse distribution with respect to four different commercial establishments (alternatives) that sell directly to the final consumer. A sensitivity analysis is conducted to test the robustness of the method. Through the analysis of a practical case, it is highlighted how the agri-food supply chain is a very complex context, in which the competitiveness of organizations is based on the ability of the decision maker to identify problems, imagine alternatives and adopt solutions. It is also highlighted that these tools, if correctly implemented in organizations, allow the start of an organizational learning process, reducing the costs associated with decision-making errors.