Elemental and inorganic nitrogen processes in soil regulate soil fertility in unfertilized soils and in agricultural plots under organic treatments. Nitrogen fixation, nitrate reduction and ammonia oxidation are three of the most important microbially mediated processes that dictate the loss and input of nitrogen in soils. However, we know very little about the distribution of these processes through the soil microscale, particularly across aggregate fractions. In this study, we investigated the distribution of the functional genes nifH (nitrogen fixation), narG (nitrate reduction) and amoA (ammonia oxidation) across aggregate fractions of three highly comparable soils. The effect of a disturbance on the community at different aggregate size-classes was also explored by comparing an untilled, a newly-tilled and a long-term tilled plot. Significant changes were observed in communities of nitrogen fixers and nitrate reducers across aggregate fractions within each soil treatment. Additionally, tillage treament proved to be disruptive of these communities at the level of every aggregate fraction. Such marked differences in communities across aggregate fractions, regardless of soil disturbance, led to further examination of the shifts in the community between individual aggregates within an aggregate fraction. Community analyses based on nifH gene and 16S rRNA composition between three individual microaggregates from the untilled plot revealed community composition (16S rRNA) shifts at this scale. However, functional shifts (nifH) were minimum when detected, indicating possible homogeneity in the role of these communities at the scale of the aggreagte fraction.