ABSTRACT This work describes the development of an intermittently aerated pilot‐scale process (V = 0.45 m3) operated for optimized efficient nitrogen removal in terms of volume, supplemental carbon and alkalinity requirements. The intermittent aeration pattern was controlled using a strategy based on effluent ammonia concentration set‐points. The unique feature of the ammonia‐based aeration control was that a fixed dissolved oxygen (DO) set‐point was used and the length of the aerobic and anoxic time (anoxic time ≥25% of total cycle time) were changed based on the effluent ammonia concentration. Unlike continuously aerated ammonia‐based aeration control strategies, this approach offered control over the aerobic solids retention time (SRT) to deal with fluctuating ammonia loading without solely relying on changes to the total SRT. This approach allowed the system to be operated at a total SRT with a small safety factor. The benefits of operating at an aggressive SRT were reduced hydraulic retention time (HRT) for nitrogen removal. As a result of such an operation, nitrite oxidizing bacteria (NOB) out‐selection was also obtained (ammonia oxidizing bacteria AOB maximum activity: 400 ± 79 mgN/L/d, NOB maximum activity: 257 ± 133 mgN/L/d, P < 0.001) expanding opportunities for short‐cut nitrogen removal. The pilot demonstrated a total inorganic nitrogen (TIN) removal rate of 95 ± 30 mgN/L/d at an influent chemical oxygen demand: ammonia (COD/NH4+‐N) ratio of 10.2 ± 2.2 at 25°C within the hydraulic retention time (HRT) of 4 h and within a total SRT of 5–10 days. The TIN removal efficiency up to 91% was observed during the study, while effluent TIN was 9.6 ± 4.4 mgN/L. Therefore, this pilot‐scale study demonstrates that application of the proposed on‐line aeration control is capable of relatively high nitrogen removal without supplemental carbon and alkalinity addition at a low HRT. Biotechnol. Bioeng. 2015;112: 2060–2067. © 2015 Wiley Periodicals, Inc. Optimization nitrogen removal in a carbon limited B‐stage was achieved through the use of intermittent aeration strategy based on online ammonia measurements.