The TRENS system is a train of biological units designed for resource recovery from wastewater. It is a sequence of a modified enhanced biological phosphorus removal and recovery system (EBP2R) coupled with a photobioreactor (PBR). The bacteria-based system constructs an optimal culture media for the downstream algae cultivation. In this work, we present a control strategy to ensure an optimal nutrient balance to feed to the PBR, so the grown algal suspension is suitable for fertigation (irrigation and fertilization of agricultural crops). The system is able to recover up to 75% of the influent load, while keeping an optimal N-toP ratio of 16 in the influent to the PBR. The system is tested under different scenarios, where the influent quality is disturbed following a step change. The control system is able to reject most of the disturbances. However, when the P-recovery is limited by the bacteria in the reactor, the control system is not able to keep the optimal phosphorus load, but only the optimal percentage recovery from the influent phosphorus. In this scenario, the system is kept under optimal conditions – in terms of nutrient balance – because the N-toP ratio is still at 16, so the green microalgae can take up most of the incoming nutrients into the PBR. The control system is able to keep the optimal phosphorus load during dynamic conditions. However when the influent nitrogen is limiting the process, the N-toP ratio drops under the optimal value. Further research is needed in order to assess the controllability of the PBR and the possible impact on the upstream operation conditions.