Conventional sequencing batch reactors (SBRs) have been developed based on nitrogen removal efficiency rather than the effluent nitrogen concentration as a design factor. The purpose of this study was to achieve the target effluent total nitrogen (TN) concentration regardless of the influent nitrogen concentration at 10 m3 pilot SBR. The desired nitrogen removal efficiency was achieved by distributing the influent one to four times in one cycle, but effluent TN concentration fluctuated as the influent nitrogen concentration varied. To achieve the target effluent TN concentration, the residual ammonia concentration after sub-feeding was adjusted to the target nitrogen concentration based on real-time ammonia sensing. When the residual ammonia concentration after sub-feeding was set at 10 or 5 mg NH4+-N L−1, the effluent TN concentration was 9.3 ± 0.6 or 4.6 ± 0.3 mg L−1, respectively, regardless of the influent TN concentration. Furthermore, complete nitrification was achieved under low temperature, from 7.2 to 13.1 °C, by controlling the aeration phase end point based on the real-time ammonia sensing. However, when the residual nitrate concentration was adjusted to a low level, the total phosphorus (TP) removal efficiency was high owing to an increase of phosphate release activity by polyphosphate accumulating organisms.