The processes of nitritation and full nitrification of synthetic reject wastewater were compared in terms of N2O and NO emissions. Two lab-scale sequencing batch reactors (SBR1 and SBR2) were enriched with Nitrosomonas (ammonia-oxidizing bacteria) and Nitrobacter (nitrite-oxidizing bacteria), as shown by fluorescence in situ hybridization (FISH) and high-resolution 16S rRNA tag pyrosequencing. Stable conversion of ammonium to nitrite and nitrite to nitrate was achieved in SBR1 and SBR2 respectively. Biomass from SBR2 was added in SBR1 in order to achieve full nitrification. Under nitritation, 1.22% of the converted-N was emitted as N2O, and 0.066% as NO. During the transition from nitritation to full nitrification, effluent nitrite concentrations decreased but nitrogen oxides were emitted at levels similar to the nitritation period. Gas emissions decreased sharply under full nitrification conditions (0.54% N2O-N/converted-N; 0.021% NO-N/converted-N), probably as a result of the combined effect of lower nitrite and ammonium concentrations in the bioreactor.