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Global concurrence is a topic that affects many companies in most sectors of the economy. In particular, the improvement in the manufacturing, packing, storage, and transportation of food has allowed farming companies from all over the world to compete for customers of a global market. In order to achieve success in this complex environment, it is convenient for the companies to be efficient even before the beginning of their business activity. This paper presents a decision support methodology for improving the design and management of an olive oil manufacturing facility based on the development of a Petri net model of the system, the simulation of its behaviour under a selected set of alternative configurations, and the choice of the most promising one by means of an optimization algorithm.