Display omitted •Continuous aeration in membrane-aerated biofilms resulted in full nitrification.•Intermittent aeration suppressed nitrite oxidation and supported anammox process.•Biofilm pH presented periodic upshifts with aeration switches.•Free ammonia speciation likely caused the inhibition of nitrite-oxidizing bacteria.•Heterotrophs established nitrous oxide-reduction zones under intermittent aeration. Membrane-aerated biofilm reactors (MABR) are being applied for autotrophic nitrogen removal, yet control of nitrogen turnover remains challenging in MABR counter-diffusion biofilms. In this study, we regulated microbial activities in two lab-scale MABRs by providing continuous versus intermittent aeration. Nitrogen consumption by different functional microbial groups was estimated from bulk measurements via a mass balance approach. Nitrite-oxidizing bacteria (NOB) proliferated under continuous aeration while they were significantly suppressed under intermittent aeration, and NOB suppression activated anaerobic ammonium oxidation. Nitritation performance in the MABR was studied through long-term bulk measurements and in situ biofilm microprofiles of dissolved oxygen (DO) and pH. During intermittent aeration pH effects rather than DO effects determined nitritation success, especially ammonia speciation, which serves as substrate and inhibitor in nitrification processes. Biofilm transition phases were monitored upon aeration switches. Canonical correspondence analysis suggested that the relative transition after anoxia and aeration intermittency were less decisive for biofilm performance than the relative aeration duration. Heterotrophic bacteria displayed minor denitrification rates with aeration control, but contributed to mitigation of nitrous oxide (N2O) emissions. N2O production hotspots were identified at the top of the anoxic biofilm zone under continuous aeration. Instead, under intermittent aeration an anoxic N2O reduction zone was established. Our observations support intermittent aeration control of MABRs as a simple strategy for energy-efficient nitrogen removal with low N2O emission. .