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Nowadays, wastewater is considered as a set of resources to be recovered rather than a mixture of pollutants that should be removed. Many resource recovery schemes have been proposed, involving the use of novel technologies whose controllability is poorly studied. In this paper we present a control structure for the novel enhanced biological phosphorus removal and recovery (EBP2R) process, which is currently under development. The aim of the EBP2R is to maximize phosphorus recovery through optimal green micro-algal cultivation, which is achieved by controlling the nitrogen to phosphorus ratio (N-to-P ratio) fed to the algae. Process control structures are developed for a sequencing batch reactor (SBR) and a continuous flow reactor system (CFS). Results, obtained using the Benchmark Simulation Model No. 1 (BSM1) dynamic input disturbance time series, suggest that the SBR can maintain a stable N-to-P ratio in the effluent (16.9 ± 0.07) and can recover about 72% of the influent phosphorus. The phosphorus recovered by the CFS is limited by the influent nitrogen (65% of the influent phosphorus load). Using the CFS configuration the effluent N-to-P ratio cannot be effectively controlled (16.45 ± 2.48). Therefore, it is concluded that the SBR is the most effective reactor configuration for the EBP2R process. Importantly, the designed control structures rely on control loops that do not require chemical dosing for nutrient management, thereby reducing the environmental footprint of the EBP2R process. The proposed control strategies can be applied to other phosphorus recovery schemes where short sludge age EBPR systems play an important role.