Due to the heterogeneous nature of soil pore structure, processes such as nitrification and denitrification can occur simultaneously at microscopic levels, making prediction of small-scale nitrous oxide (N₂O) emissions in the field notoriously difficult. We assessed N₂O+N₂ emissions from soils under maize (Zea mays L.), switchgrass (Panicum virgatum L.), and energy sorghum (Sorghum bicolor L.), three potential bioenergy crops in order to identify the importance of different N₂O sources to microsite production, and relate N₂O source differences to crop-associated differences in pore structure formation. The combination of isotopic surveys of N₂O in the field during one growing season and X-ray computed tomography (CT) enabled us to link results from isotopic mappings to soil structural properties. Further, our methodology allowed us to evaluate the potential for in situ N₂O suppression by biological nitrification inhibition (BNI) in energy sorghum. Our results demonstrated that the fraction of N₂O originating from bacterial denitrification and reduction of N₂O to N₂ is largely determined by the volume of particulate organic matter occluded within the soil matrix and the anaerobic soil volume. Bacterial denitrification was greater in switchgrass than in the annual crops, related to changes in pore structure caused by the coarse root system. This led to high N-loses through N₂ emissions in the switchgrass system throughout the season a novel finding given the lack of data in the literature for total denitrification. Isotopic mapping indicated no differences in N₂O-fluxes or their source processes between maize and energy sorghum that could be associated with the release of BNI by the investigated sorghum variety. The results of this research show how differences in soil pore structures among cropping systems can determine both N₂O production via denitrification and total denitrification N losses in situ.