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This study deals with the effect of aeration control strategies on the nitrogen removal efficiency and nitrous oxide (N₂O) emissions in a partial nitritation–anammox reactor with granular sludge. More specifically, dissolved oxygen (DO) control, constant airflow and effluent ammonium (NH₄⁺) control strategies were compared through a simulation study. Particular attention was paid to the effect of flocs, which are deliberately or unavoidable present besides granules in this type of reactor. When applying DO control, DO setpoints had to be adjusted to the amount of flocs present in the reactor to maintain high nitrogen removal and reduce N₂O emissions, which is difficult to realize in practice because of variable floc fractions. Constant airflow rate control could maintain a good nitrogen removal efficiency independent of the floc fraction in the reactor, but failed in N₂O mitigation. Controlling aeration based on the effluent …