A novel feedforward-feedback control strategy was developed for complete autotrophic nitrogen removal in a sequencing batch reactor. The aim of the control system was to carry out the regulation of the process while keeping the system close to the optimal operation. The controller was designed based on a process model and then tested experimentally. The resulting batch-to-batch control strategy had the total nitrogen removal efficiency as controlled variable and the setting of the aeration mass flow controller as manipulated variable. Compared to manual operation mode (constant air supply), the controller resulted in a significant performance improvement: removal efficiency was kept at a stable high level in the presence of influent ammonium concentration disturbances, and the absolute deviation on removal efficiency was reduced by 40%. The successful validation of the controller in a lab-scale reactor is a promising result, which brings this control strategy one step closer to full-scale implementation. (C) 2014 Elsevier B.V. All rights reserved.