This paper presents a management system for a fleet of autonomous mobile robots performing logistics in security-heterogeneous factories. Loading and unloading goods and parts between workstations in these dynamic environments often demands from the mobile robots to share space and resources such as corridors, interlocked security doors and elevators among themselves. This model explores a dynamic task scheduling and assignment to the robots taking into account their location, tasks previously assigned and battery levels, all the while being aware of the physical constraints of the installation. The benefits of the proposed architecture were validated through a set of experiments in a mockup of INCM's shop-floor environment. During these tests 3 robots operated continuously for several hours, self-charging without any human intervention.