While Cluster-Tree network topologies look promising for WSN applications with timeliness and energy-efficiency requirements, we are yet to witness its adoption in commercial and academic solutions. One of the arguments that hinder the use of these topologies concerns the lack of flexibility in adapting to changes in the network, such as in traffic flows.This paper presents a solution to enable these networks with the ability to self-adapt their clusters’ duty-cycle and scheduling, to provide increased quality of service to multiple traffic flows. Importantly, our approach enables a network to change its cluster scheduling without requiring long inaccessibility times or the re-association of the nodes. We show how to apply our methodology to the case of IEEE 802.15.4/ZigBee cluster-tree WSNs without significant changes to the protocol. Finally, we analyze and demonstrate the validity of our methodology through a comprehensive simulation and experimental validation using commercially available technology on a Structural Health Monitoring application scenario.