The global environment, where many companies compete for their survival, requires a continuous adaptation to changes in the market and to other environment variables. Food industry, agriculture in particular, is a field where the companies are especially sensitive to modifications in regulations and market requirements. It is very convenient to provide the companies of this sector with a theoretical basis, as well as with practical tools for developing an efficient management that may guarantee not only their survival but also their success. In this area, decision-support systems based on the simulation of models, developed by means of the paradigm of the Petri nets, can offer a significant help for improving the efficiency of farming companies, based on the appropriate decision making. In this article, a methodology for decision making, supported by artificial intelligence, is applied to the farming field and an application case is analyzed for better understanding of the advantages and drawbacks of this approach. In particular, a decision-making methodology for improving the management of the operation and redesign of traditional companies in the farming industry is applied to the wine sector in the region of La Rioja (Spain).