Pesticides are applied to agricultural systems in high quantities relative to other synthetic compounds and therefore have considerable effects on soil microbial communities and their functions. Although pesticides undergo considerable evaluation for efficacy in controlling target pests in agroecosystems and non-agricultural sites, effects on soil and environmental organisms and their activities receive minimal attention beyond specific environmental impacts required by regulatory agencies. Limited research has found that pesticides used in agricultural management systems influence both structural and functional biodiversity in soils, which are important components of soil health. The objectives of this chapter are to present the mechanisms by which pesticides affect soil microbial diversity and describe management systems developed to limit impacts of pesticides on soil and environmental health.