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The adoption of industrial cyber-physical systems is facing several challenges, with artificial intelligence and self-organization techniques assuming critical aspects to be considered in the deployment of such solutions to support the dynamic evolution and adaptation to condition changes. This paper describes the implementation of a modular, flexible and self-organized cyber-physical conveyor system build up with different individual modular and intelligent transfer modules. For this purpose, multi-agent systems are used to distribute intelligence among transfer modules supporting pluggability and modularity, complemented with self-organization capabilities to achieve a truly self-reconfigurable system. Furthermore, Internet of Things and Artificial Intelligence technologies are used to enable the real-time monitoring of the system, aiming the detection and prevention of anomalies in advance, and to enable the protection from possible external threats.