Agriculture is the main source of terrestrial N2O emissions, a potent greenhouse gas and the main cause of ozone depletion. The reduction of N2O into N2 by microorganisms carrying the nitrous oxide reductase gene (nosZ) is the only known biological process eliminating this greenhouse gas. Recent studies showed that a previously unknown clade of N2O-reducers (nosZII) was related to the potential capacity of the soil to act as a N2O sink. However, little is known about how this group responds to different agricultural practices. Here, we investigated how N2O-producers and N2O-reducers were affected by agricultural practices across a range of cropping systems in order to evaluate the consequences for N2O emissions. The abundance of both ammonia-oxidizers and denitrifiers was quantified by real-time qPCR, and the diversity of nosZ clades was determined by 454 pyrosequencing. Denitrification and nitrification potential activities as well as in situ N2O emissions were also assessed. Overall, greatest differences in microbial activity, diversity, and abundance were observed between sites rather than between agricultural practices at each site. To better understand the contribution of abiotic and biotic factors to the in situ N2O emissions, we subdivided more than 59,000 field measurements into fractions from low to high rates. We found that the low N2O emission rates were mainly explained by variation in soil properties (up to 59%), while the high rates were explained by variation in abundance and diversity of microbial communities (up to 68%). Notably, the diversity of the nosZII clade but not of the nosZI clade was important to explain the variation of in situ N2O emissions. Altogether, these results lay the foundation for a better understanding of the response of N2O-reducing bacteria to agricultural practices and how it may ultimately affect N2O emissions.