Lean Manufacturing (LM) is a methodology focused on improving performance and operational efficiency in industries by eliminating waste, such as in the dairy industry. This research aims to model, analyze, visualize, and propose improvements in the performance of the cheese production process using the FlexSim simulation software. The methodology employed is experimental, obtaining data that is analyzed with the different tools of the soft-ware, such as Fluid, Process Flow, Expert-Fit, and Experimenter. In this sense, the analysis of the activities involved in the current state of the company’s process flow is conducted through a Value Stream Mapping (VSM). Additionally, the analysis and implementation of LM with tools such as 5S and Just in Time (JIT) within the simulation model has managed to reduce non-value-adding waste, such as waiting times, unnecessary movements, and transportation during different stages of production, proposing methods to eliminate them. Then, possible improvement scenarios were generated using the Experimenter tool to identify the bottleneck and demonstrate a 23.8% performance improvement. This translates into increased capacity and efficiency, replicable by other companies, even in other industrial sectors, to improve operational decision-making.