Determining success factors for managing supply chains is a relevant aspect for companies. Then, modeling the relationship between inventory cost savings and supply chain success factors is a route for stating such a determination. This is particularly important in pharmacies and food nutrition services (FNS), where the advances made on this topic are still scarce. In this article, we propose and formulate a robust compromise (RoCo) multi-criteria model based on non-linear programming and time-dependent demand. The novelty of our proposal is in defining a score that allows us to measure the mentioned success factors in a simple way, in meeting together all three elements (RoCo multi-criteria, non-linear programming, and time-dependent demand) to state a new model, and in applying it to pharmacies and FNS. This model relates inventory cost savings for pharmacy/FNS and success factors across their supply chains. Savings of inventory costs are predicted by lot sizes to be purchased and computed by comparing optimal and true inventory costs. We utilize a system that records the movements and costs of products to collect the data. Factors, such as purchasing organization, economies of scale, and synchronized supply, are assumed using the purchase system, with these factors ranked on a Likert scale. We consider multilevel relationships between savings obtained for 79 pharmacy/FNS products, and success factor scores according to these products. To deal with the endogeneity bias of the relationships proposed, internal instrumental variables are employed by utilizing generalized statistical moments. Among our main conclusions, we state that the greatest cost savings obtained from inventory models are directly associated with low-success supply chain factors. In this association, the success factors operate as endogenous variables, with respect to inventory cost savings, given the simultaneity of their relationship with cost savings when inventory decision-making.