The fourth industrial revolution features smart and connected technologies that improve significantly business operations. Certainly, there is an increase of efficiency and productivity of smart factories due to the implementation of these innovative technologies. Nevertheless, this new industrial model threatened the need of human operators, as the implemented smart systems are capable of executing and controlling autonomously manufacturing operations. However, in many cases, the inherent characteristics of certain processes challenge these systems when the operator is incorporated in the automated manufacturing processes. In fact, these systems lack of assuring the well-being of the human operators. This paper introduces a framework of a manufacturing control system that integrates human activities in the manufacturing process, in order to minimize the degradation of the operator’s well-being. This approach employs a human decisional entity as a virtual component – a holon that monitors the well-being indicators of the operator and allocates the tasks in real-time during production execution. The case study analysed in this paper is executed in a simulated flexible manufacturing system with two workstations for inspections, one being fully conducted by the operator and the other by a computer vision system. In this exploratory research, the experiments evaluate the role and cooperative behaviour of the human decisional entity and illustrate the integration of the operator in the systems.