The escalation of industrial as well as agricultural enactment substantially the use of pesticides has made our natural resources absolutely sunken and has severely affected the biodiversity and ultimately soil health. Concern has been raised over the long term sustainability and environmental consequences due to intensification of agro-ecosystem. In Punjab, the intensive rice-wheat systems have started to decipher the signs of serious decline associated with loss of soil quality and increased plant health problems [1]. Pesticides enter the soil by direct supplementation (agricultural practices) or by indirect methods (discharge from production sites, accidental spillage, leakage from pesticide dump sites, surface run off, etc.). Pesticides are known to affect the behavior of soil enzymatic system that plays an important role in soil-plant biological activity [2]. The residues of pesticides prevalent in environmental matrices are of larger concern [3]. Fertilizer and pesticide usage tend to elevate the level of nutrients in soil and simultaneously increasing toxins in water and soil. Excessive use of pesticides and fertilizers also pollute the surrounding environment in addition to deteriorating the physical and chemical properties of soil [4]. The usage of such pesticides and fertilizers often leads to a reduction in total microbial activity, porosity, particle and bulk density of soil [4] and excessive leaching of nutrients resulting in salinity induced plant stress [5,6]. Vermicompost on the other hand is basically a complex mixture of fecal matter of earthworm’s humified organic matter and microorganisms. Supplementation of vermicompost in soil or plant growth media leads to increased germination, elevates growth, flowering, and accelerates the production of fruit. Vermicompost helps in maintaining the soil structure healthy by altering the physico-chemical properties of soil [7]. Vermicompost plays an important role in increasing the size, biodiversity and activity of microbes in the soil [4]. It is also a great source of nutrients and organic matter and retains it for a longer period of time without any harmful effect on the environment [8]. It contains high level of plant growth hormones and soil enzymes [9]. Usage of vermicompost may lead to fine tuning of input nutrients and plant needs and thus has maximized yields. Allium cepa is used as a test material to determine genotoxic effects of different chemicals. Environmental agencies like the United Nations Environmental Program, World Health Organization, International Program on Plant Bioassay and US Environmental Protection Agency have advocated and validated the use of plants as test organisms [10]. Allium genus, especially the use of A. cepa for bio-monitoring of genotoxicity is considered to be very efficient [11]. This assay has been utilized to detect genotoxicity of various products like pressmud, waste water sludge, distillery sludge, etc. The present paper has embarked on two major aspects: (i) the effect of pesticides on the genotoxicity of A. cepa and (ii) the effect of vermicompost on A. cepa. This study also focuses on the dynamics of the pesticides present in the agricultural farmlands that are deteriorating the crop quality. Altogether, there is a dire need of a healthy ecosystem that provides with fertile soil, clean water, food and other natural resources [9]. Thus, the evaluation of agricultural soils for detection of their potency to risk biodiversity and ecological systems is obligatory. In this approach the effect of the bioavailable fractions of pollutants/chemicals present in the complex soil matrix was taken into account.