The lack of process standardization and formal management tools in animal feed plants can lead to operational variability, negatively affecting production efficiency and final product quality. This study aims to optimize the performance of the operational system of an animal feed plant through the implementation of process standardization, quality assurance, and lean manufacturing tools. The study was conducted under an applied approach using a case study at the “El Aire” animal feed plant, located in the state of Jalisco, Mexico. The methodology was structured in three phases: process standardization through procedure manuals, flowcharts, and Standard Operating Sheets; strengthening of the quality system through technical specifications and a quality control plan; and implementation of the 5S methodology to improve operational environment conditions. The results show a significant improvement in the control of the production system, reflected in an increase in the level of process documentation, improvements in critical product quality parameters, and an increase in the level of order and cleanliness in operational areas, which rose from an average of 16% to 85%. These actions contributed to greater efficiency in operational execution and improved compliance with production schedules. It is concluded that the structured and progressive application of standardization and lean manufacturing tools strengthens operational management in animal feed plants, even in highly automated environments, providing a solid foundation for continuous improvement and the sustainability of the production system.