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Free ammonia (FA) inhibition has been taken advantage as a strategy to suppress the growth of nitrite‐oxidizing bacteria (NOB) in aerobic granules stabilized in a continuous upflow airlift reactor to achieve partial nitritation. However, after nearly 18 months of continuous exposure of aerobic granules to FA in the reactor, the FA inhibition of NOB was proven ineffective, and the partial nitritation gradually shifted to partial nitrification even though the long‐term granule structural stability remained excellent under the continuous‐flow mode. The extent of NOB resistance to FA inhibition was quantified based on the kinetic response of NOB to various FA concentrations in the form of an uncompetitive inhibition coefficient. It was confirmed that the NOB immobilized in larger granules under longer term exposure to FA tend to become more resistant to FA. Thereby, it was concluded that NOB can develop strong resistance to FA after continuous exposure, and thus, FA inhibition is not a reliable strategy to achieve partial nitritation in mainstream wastewater treatment. Practitioner points Nitrifying aerobic granules can remain structurally stable in continuous‐flow bioreactors. NOB developed free ammonia resistance after 6‐month continuous exposure. Larger aerobic granules tended to develop stronger free ammonia resistance. Free ammonia inhibition is not a reliable strategy for mainstream anammox.