Water in soil is known to be a key factor for controlling N2O emissions because N2O is mainly produced by denitrification in anoxic environments. In this study, we proposed a methodology to image the water and soil structure of a soil sample with X-ray computed tomography while controlling the hydric state and monitoring N2O fluxes. We used a multistep outflow system to apply two wetting–drying cycles to an undisturbed soil. The soil core was scanned with coarse-resolution X-ray computed tomography, one time during wetting and several times during drying, to measure quantitative and qualitative indicators of the pore network. Nitrous oxide emissions were higher during the first (C1) than during the second (C2) wetting–drying cycle for both the wetting and the drying phases. Fluxes increased quickly after the beginning of the drying phase to reach a peak after 5 h. Differences in the intensity of N2O emissions between the two cycles were attributed to differences in the water saturation, air-phase connectivity, and relative gas diffusion coefficient, which led to more or less N2O production, consumption, and entrapment in the soil. The speed of the N2O emissions at the beginning of the drying phase depended on the rate of increase of the air-filled pore volume and connectivity, and was especially well described by the estimated relative gas diffusion coefficient. Parameters of the soil structure were not able to explain completely the intensity of N2O emissions during drying; N2O production and consumption factors were also involved.