Nitrous oxide (N2O) is a potent greenhouse gas, which is mainly produced from agricultural soils. Ammonia oxidation is the rate-determining step in N2O production, and the process is carried out by ammonia oxidizers, bacteria and archaea. Soil aggregate size has been shown to alter soil properties, which affect N2O emissions and bacterial communities. However, the effect of aggregate size on temporal and total N2O emissions and ammonia-oxidizing bacteria (AOB) and archaea (AOA) is not fully understood. This incubation study investigated the effect of three different soil aggregate sizes on N2O emissions and ammonia oxidizer abundance under high urine-N concentrations and the effectiveness of a nitrification inhibitor, dicyandiamide (DCD), at reducing N2O emissions in different aggregate soils. It was found that temporal patterns of N2O emissions were affected by aggregate size with higher peak emissions in the large and medium aggregates. However, the total emissions were the same due to a ‘switch’ in emissions at day 66, after which smaller aggregates produced higher N2O emissions. It is suggested that the switch was caused by an increase in aggregate disruption in the small aggregates, following the urine application, due to their higher surface area to volume ratio. AOB and AOA abundances were not significantly affected by aggregate size. DCD was effective in reducing N2O emissions in all aggregate sizes by an average of 79%. These results suggest that similar ammonia oxidizer abundance is found in soils of different aggregate sizes, and the efficacy of DCD in reducing N2O emissions was not affected by aggregate size of the soil.