Soil contamination has enlarged over the decades due to intensive use of pesticides and chemical fertilizers in agronomy. Earthworms are significant organisms in the soil community. Earthworms are the major role in soil fertility in most ecological system and the production of biogenic structures. Moreover, earthworm gut mucus enhances the beneficial soil microorganism potential biological activities. They are used as model organisms for assessing the ecological risks of chemicals. Enrichment of essential nutrients in soil through earthworm is a cost-effective and eco-friendly approach. In India, the organophosphorus pesticide monocrotophos is commonly used to control agricultural pests. Hence, it is important to study the effect of monocrotophos on the gut microbiota in Lampito mauritii. A 15-day exposure to a low (1/10th of the LC50 after 96 h i.e., 0.093 ppm kg−1) and high sublethal concentration (1/3rd of the LC50 after 96 h i.e., 0.311 ppm kg−1) of monocrotophos led to reduced proliferation of the gut microbiota in L. mauritii. However, exposure for 30 days led to a recuperation of the microbial populations to near control values. Among the eight bacterial and five fungal species that inhabit the gut of L. mauritii, only six bacterial and three fungal species were able to survive after exposure to monocrotophos. In addition to the study, histopathological changes were observed in the intestine of L.mauritii after application of lower sublethal concentration of monocrotophos. Severe pathological changes such as vacuolization, degenerated nuclei, damaged villi and congestion of the blood sinuses were noticed in the intestine on 1st and, 5th day of the experiment. But in 30th day the damages were slowly recovered due to degradation of monocrotophos by the presence of some pesticides degrading bacterial and fungal species and regenerative capability of chloragogen cells in the intestine. The results suggested that reduced microbial populations and pathological damages in intestine were observed during the application of monocrotophos. So, the monocrotophos have several harmful impacts on earthworms.