The extensive use of pesticides in agricultural production can degrade and damage the community of microorganisms living in the soil, particularly when these chemicals are overused or misused as chemical compounds build up in the soil. The full impact of pesticides on soil microorganisms is still not entirely understood; many studies have found deleterious effects of pesticides on soil microorganisms and biochemical processes, while others have found that the residue of some pesticides can be degraded and assimilated by microorganisms. The effect of pesticides on soil microorganisms is impacted by the persistence, concentration, and toxicity of the applied pesticide, in addition to various environmental factors. This complex interaction of factors makes it difficult to draw definitive conclusions about the interaction of pesticides with the soil ecosystem. In general, long-term pesticide application can disturb the biochemical processes of nutrient cycling.

Many of the chemicals used in pesticides are persistent soil contaminants, whose impact may endure for decades and adversely affect soil conservation.

The use of pesticides decreases the general biodiversity in the soil. Not using the chemicals results in higher soil quality, with the additional effect that more organic matter in the soil allows for higher water retention. This helps increase yields for farms in drought years, when organic farms have had yields 20-40% higher than their conventional counterparts. A smaller content of organic matter in the soil increases the amount of pesticide that will leave the area of application, because organic matter binds to and helps break down pesticides.

Degradation and sorption are both factors which influence the persistence of pesticides in soil. Depending on the chemical nature of the pesticide, such processes control directly the transportation from soil to water, and in turn to air