The livelihood of the entire population and the existence of farming communities is solely dependent on agriculture. Fertility of the soil is governed by its texture and diversified fauna present in the soil medium. Various agricultural inputs are applied with the eventual aim to achieve the highest productivity whereas hazardous effects on soil microorganisms are often ignored. Pesticides are noxious chemicals used to mitigate crop losses incurred by nematodes, insects, weeds, mites, and pathogens. Fungicides modify the fungi communities accountable for the nutrient recycling in the soil, especially copper-based fungicides which cause harmful effects on earthworms. The continuous use of herbicides indirectly reduces the associated arthropod communities. Insecticides cause toxic effects on most of the lower soil invertebrates and cause negative impact on their growth and development and alter the trophic structure in their habitats. Buildup of synthetic pesticides in the soil cause many sublethal effects on the existing natural fauna and affects their survival. However, pesticides help in diminishing the quantitative losses caused by pests and enhance the agricultural productivity, but consequently the cost of enhanced productivity is compensated by the Earth’s ecosystems. This review provides insight into the effects of pesticides on the soil health.