Pesticides are the group of chemicals used in agriculture for the control of weeds, insects, pathogens, nematodes, rodents, etc. Globally, among the pesticide’s application, herbicides occupy the major share (52%) followed by insecticides (24%) and fungicides (23%). Though the pesticides application is helpful in global food production, the indiscriminate application of pesticides in agriculture severely affects not only the soil but also the water bodies and the surrounding ecosystem. It causes environmental pollution, deterioration of soil, plant, and animal health, and negative impact on climate change. In this review, the interplay between pesticides application, soil health, carbon sequestration, and climate change is being discussed. Similarly, the role of soil microorganisms in mitigating the negative effect of pesticides has been highlighted. The review also recommends certain future course of action and mitigation strategies.