Pesticides including insecticides are applied in agricultural practices to control insect pests. However, their excessive usage often poses a severe threat to the growth, physiology, and biochemistry of plants. Here, responses of chickpea and greengram seedlings exposed to three fipronil (FIP) concentrations i. e. 100 (1×), 200 (2×) and 300 (3×) μg mL−1 was evaluated under in vitro. Among doses, 3× had a greater negative impact on germination attributes, root-shoot elongation, vigor indices, length ratios, and survival of seedlings. Besides, the morphological distortion in root tips, oxidative stress generation, and cellular death in fipronil-supplemented root seedlings were observed under scanning electron (SEM) and confocal laser scanning (CLSM), respectively. A significant (p ≤ 0.05) and pronounced upsurge in plant stressor metabolites such as proline, malondialdehyde (MDA), electrolyte leakage (EL), hydrogen peroxide (H2O2) content, and antioxidants enzymes in plant seedlings further confirmed the fipronil toxicity. In addition, a concentration-dependent decrease in respiration efficiency (RE) and ATP content in FIP-treated seedlings was observed. Reduced mitotic index (MI) and numerous chromosomal anomalies (CAs) in root meristematic cells of seedlings are a clear indication of insecticide-induced cytotoxicity. Furthermore, a dose-dependent increase in DNA damage in root meristematic cells of greengram revealed the genotoxic potential of fipronil. Conclusively, fipronil suggested phyto and cyto-genotoxic effects that emphasize their careful monitoring in soils before application and their optimum addition in soil-plant systems. It is high time to prepare both target-specific and slow-released agrochemical formulations for crop protection with concurrent safeguarding of the soil.