Denitrifying phosphorus removal was realized in sequencing batch reactors using different carbons sources (acetate, propionate, and a mixture of acetate/propionate).Nutrient removal and N2O production were investigated, and the factors affecting N2O production were explored. Nitrogen removal was 40.6% lower when propionate was used as the carbon source instead of acetate, while phosphorus removal was not significantly different. N2O production was greatly reduced when propionate was used as the carbon source instead of acetate. The emission factor in the propionate system was only 0.43%, while those in the acetate and mixed-carbon source system were 16.3% and 1.9%, respectively. Compared to the propionate system, ordinary heterotrophic organisms (i.e., glycogen-accumulating organisms) were enriched in the acetate system, explaining the higher N2O production in the acetate system. The lower nitrite accumulation in the propionate system compared to the acetate system was the dominant factor leading to the lower N2O production.