Autotrophic ammonium oxidation in membrane-aerated biofilm reactors (MABRs) can make treatment of ammonium-rich wastewaters more energy-efficient, especially within the context of short-cut ammonium removal. The challenge is to exclusively enrich ammonium-oxidizing bacteria (AOB). To achieve nitritation, strategies to suppress nitrite-oxidizing bacteria (NOB) are needed, which are ideally grounded on an understanding of underlying mechanisms. In this study, a nitrifying MABR was operated under intermittent aeration. During eight months of operation, AOB dominated, while NOB were suppressed. On the basis of dissolved oxygen (DO), ammonium, nitrite, and nitrate profiles within the biofilm and in the bulk, a 1-dimensional nitrifying biofilm model was developed and calibrated. The model was utilized to explore the potential mechanisms of NOB suppression associated with intermittent aeration, considering DO limitation, direct pH effects on enzymatic activities, and indirect pH effects on activity via substrate speciation. The model predicted strong periodic shifts in the spatial gradients of DO, pH, free ammonia, and free nitrous acid, associated with aerated and nonaerated phases. NOB suppression during intermittent aeration was mostly explained by periodic inhibition caused by free ammonia due to periodic transient pH upshifts. Dissolved oxygen limitation did not govern NOB suppression. Different intermittent aeration strategies were then evaluated for nitritation success in intermittently aerated MABRs: both aeration intermittency and duration were effective control parameters.