The objective of this work was to measure the fluxes of N2O-N and NH3-N throughout the growing season of irrigated common-bean (Phaseolus vulgaris), as affected by mulching and mineral fertilization. Fluxes of N2O-N and NH3-N were evaluated in areas with or without Congo signal grass mulching (Urochloa ruziziensis) or mineral fertilization. Fluxes of N were also measured in a native Cerrado area, which served as reference. Total N2O-N and NH3-N emissions were positively related to the increasing concentrations of moisture, ammonium, and nitrate in the crop system, within 0.5 m soil depth. Carbon content in the substrate and microbial biomass within 0.1 m soil depth were favoured by Congo signal grass and related to higher emissions of N2O-N, regardless of N fertilization. Emission factors (N losses from the applied mineral nitrogen) for N2O-N (0.01–0.02%) and NH3-N (0.3–0.6%) were lower than the default value recognized by the Intergovernmental Panel on Climate Change. Mulch of Congo signal grass benefits N2O-N emission regardless of N fertilization.