Flexible Manufacturing Systems (FMSs) offer greater flexibility, efficiency, and automation in manufacturing. However, it remains a challenge to improve, manage and optimize production. This article explores the use of Multi-Agent Systems (MASs) as a tool to address these challenges. A review of recent advances in the application of MAS to FMS and Industry 4.0 is made, including dynamic assignment of tasks to robots based on real-time conditions; coordination of multiple robots, allowing collaboration between them to improve performance; and adaptability to changing environments, allowing the system to adjust to dynamic production demands and unforeseen situations. A case study that demonstrates the application of MAS for cooperative decision-making in a three-robot FMS system is presented. It is appropriate for improving efficiency, flexibility, coordination, and overall decision-making capabilities within a FMS environment. With this, MAS enables production optimization, leading to smarter, more adaptable, and more efficient manufacturing processes.