Modern manufacturing systems are expected to be flexible and efficient in order to cope with challenging market demands. Thus, they must be flexible enough as to meet changing requirements such as changes in production, energy efficiency, performance optimization, fault tolerance to process or controller faults, among others. Demanding requirements can be defined as a set of quality of service (QoS) requirements to be met. This paper proposes a generic and customizable multi-agent architecture that, making use of distributed agents, monitors QoS, triggering, if needed, a reconfiguration of the control system to recover QoS. As a proof of concept, the architecture has been implemented to provide availability of the control system understood as service continuity. The prototype has been tested in a case study consisting of an assembly cell where assessment of the approach has been conducted.