Effect of methanol and glycerol on nitrous oxide (N2O) emission in two laboratory-scale modified Ludzak Ettinger (MLE) processes was investigated during three distinct periods: dissolved oxygen (DO) control by intermittent aeration with a DO controller, and high and low aeration rates. N2O consumption rate in an anoxic tank and aeration mode influenced N2O emission rates from the MLE processes. In the DO control period, N2O emission rate from the glycerol-fed MLE process was higher than the methanol-fed counterpart, likely caused by a higher N2O consumption rate in an anoxic tank of the methanol-fed process. During the period of a higher aeration rate, N2O emission rates from both processes were comparable. In contrast, during the period of a lower aeration rate, N2O emission rate from the methanol-fed MLE process was higher than that from the glycerol-fed counterpart likely because of a higher degree of nitrite accumulation, corroborated by statistical analysis. N2O consumption activities of biomasses fed with the different carbon sources were distinct. However, the high activity did not necessarily result in a decrease in N2O emission rate from an aerobic tank and the effect of nitrite on the emission was stronger under the tested conditions.