The paper addresses the problem of modelling a FMS with random recipes and controlling it with an agent-based architecture. One of the features of the system are the random recipes, i.e. recipes that are unknown a priori for the control system, which represent a high flexible-routing class of FMS. In particular, a PN model able to represent both the mechanism of generation of random recipes and then the execution of such randomly generated recipe is shown. The obtained formal model is then studied to develop suitable control policies, e.g. against deadlocks. Then, such a model, is implemented in one of the most popular agent platforms, JADE (Java agent development framework)