A novel sequencing aerated biofilm reactor (SABR) was designed for effective nitrogen removal from onsite wastewater with a footprint 10 times smaller than conventional drainfield and a high hydraulic capacity. The study examined the effect of aeration pattern, wastewater strength, and carrier type on N-removal performance. Over 93 % COD removal and > 80 % TN-removal was achieved in the SABR integrated with a polishing unit (10 % woodchips, v/v) at the optimized aeration pattern (4-h pre-anoxic, 7 aeration cycles of 20 min aeration per hour at 1 L-air/min airflow rate, 1 h post-anoxic). Carriers' shape and surface area did not impact SABR's N-removal performance (31.8 % vs. 28.2 %). The optimal operation conditions obtained in bench-scale SABR tests were pilot tested with the 10 % woodchip polishing unit. Efficient TN-removal (72.4 %) was achieved with low effluent TN concentrations (6.5 ± 3.9 mg-N/L) by the pilot SABR. Ammonium (NH4+) was the predominant N-species (5.5 ± 6.0 mg-N/L) in the final effluent while NOx− was constantly below the detection limit (< 0.05 mg-N/L). Quantitative PCR analysis of functional genes involved in N-removal (amoA-AOA, amoA-AOB, nirS, nirK and nosZ) were comparable for bench-scale and pilot-scale SABRs and revealed higher abundance of amoA-AOB (> 4 orders of magnitudes higher than amoA-AOA) and nirS (nirK/nirS: 0.2–1.8 × 10−2), suggesting amoA-AOB and nirS may serve as biomarkers to monitor the system performance. Collectively, the results suggest that SABR offers a versatile approach to treat wastewater at various strengths and is applicable in areas with space constraints, shallow groundwater, and sensitive water bodies.