Nitrogen removal, nitrous oxide (N 2 O) emission and microbial community in sequencing batch and continuous-flow intermittent aeration processes were investigated. Two sequencing batch reactors (SBRs) and two continuous-flow multiple anoxic and aerobic reactors (CMRs) were operated under high dissolved oxygen (DO)(SBR-H and CMR-H) and low DO (SBR-L and CMR-L) concentrations, respectively. Nitrogen removal was enhanced under CMR and low DO conditions (CMR-L). The highest total inorganic nitrogen removal efficiency of 91.5% was achieved. Higher nitrifying and denitrifying activities in SBRs were observed. CMRs possessed higher N 2 O emission factors during nitrification in the presence of organics, with the highest N 2 O emission factor of 60.7% in CMR-L. SBR and low DO conditions promoted N 2 O emission during denitrification. CMR systems had higher microbial diversity. Candidatus Accumulibacter, Nitrosomonadaceae and putative denitrifiers (N 2 O reducers and producers) were responsible for N 2 O emission.