Soils under agriculture are the largest anthropogenic source of nitrous oxide (N2O), an important greenhouse gas and ozone-depleting substance. Reducing N2O emissions from soils under agriculture without compromising crop production is an emerging goal of soil-health management. Soil mesofauna are integral soil components in virtually all terrestrial ecosystems but have been historically neglected in soil-health management. However, our previous studies demonstrated that fungivorous mites, the numerically dominant members of soil mesofauna, could be used as natural agents to mitigate soil N2O emissions. We found that fungivorous mites can exert remarkable top-down forces that can suppress the biomass of fungal N2O producers and thus negatively regulate fungal N2O production. Furthermore, we found that the application of coconut husks, the low-value part of coconut that is commonly used as a soil conditioner in agriculture, to soil can provide a favourable habitat for fungivorous mites due to its porous structure, thereby increasing mite abundance in agricultural fields. Based on this method, the grazing forces of fungivorous mites could be artificially enhanced, thereby reducing N2O emissions, especially those dominated by fungal denitrification. These results demonstrate that maintaining the integrity of the soil mesofaunal communities should be considered in future soil-health management to mitigate N2O emissions.