Soil microbial communities are functionally diverse, responding to distal and proximal regulators of activity and functioning on multiple temporal and spatial scales due to the complex heterogeneity of the soil system. Soil microbial denitrifying and nitrifying communities drive terrestrial N2O emissions. Research was conducted on the effects of agricultural management on these communities in order to develop guidelines on agricultural practices which may mitigate these emissions. Climate and associated changes in the soil environment were large drivers of these communities, with results of multi-year studies indicating that differences in temperature and soil moisture distinctly affected the size of denitrifier communities. Choice of annual vs. perennial biomass crops, and the harvesting practices used in perennial systems also affected the size of these communities, and residue return increased the activity of the N2O-reducing community over a growing season. Next-generation sequencing was used to link changes in the structure of nitrifier and denitrifier communities with agricultural practices that were associated with differences in field-scale N2O fluxes; specific indicator operational taxonomic units (OTUs) and nosZ gene abundances were largely responsible for driving differences in these communities. Analysis of nitrifier and denitrifier communities paired with changes in N isotopes gave complementary inferences about the production mechanisms of N2O in the field. Together, this body of research gives a comprehensive picture of the many factors that affect the functioning of these communities, and indicates that management practices influence the abilities of these communities to produce and consume N2O. Future research focusing on linking changes in nitrifier and denitrifier soil microbial communities with agricultural management and associated N2O fluxes within specific climatic regions, geographies, and soil types is required in order to better understand the mechanisms controlling these communities and how these communities may be manipulated through management choices to mitigate soil N2O emissions.