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Membrane‐aerated biofilm reactors (MABRs) are being increasingly being implemented at full‐scale for domestic wastewater treatment and effective biofilm control is critical to their performance. This study investigated the impact of three biofilm scouring strategies on nitrogen removal performance of a pilot‐scale MABR operated in Houston, TX: (1) regular air scouring, (2) high intensity air scouring, and (3) high liquid flow scouring. Normal and high intensity air scouring regimes and a high liquid flow scour (10× baseline flow) were each tested sequentially. High NH₄⁺‐N removal efficiency of 52% in flow‐through mode was observed post‐high liquid flow scouring, which was comparable to the performance during the intense scouring regime. The absolute abundance ofamoAgene for ammonia oxidizing bacteria (AOB) increased significantly by over 200%, between pre‐ and post‐high liquid flow scouring. The energy consumption was 43% lower for the combination of high liquid flow scouring with regular air scouring as compared to the intense air scouring. This study showed that high liquid flows may be utilized as an energy‐efficient biofilm control strategy in nitrifying MABR systems. Practitioner PointsPilot‐scale MABR reactors were operated with different scouring settings: regular aeration, intense aeration, and high liquid flow.High liquid flow scouring improved nitrification efficiency, comparable to intense scouring.High liquid flow scouring selected for nitrifiers as seen by an increase in AOB quantified asamoAgene abundance.Using high liquid flow with regular aeration scouring reduces electrical energy consumption by 43% as compared to intense aeration scouring.High liquid flows may be used as an energy‐efficient biofilm control strategy to improve nitrification performance in MABR systems.