Heavy metal (HM) and metalloid exposure induces oxidative stress in plants resulting in growth inhibition and cellular damage. This study investigated the phytotoxic and genotoxic effects of cadmium (Cd2⁺), chromium (Cr⁶⁺), and arsenic (As3⁺) on Capsicum annuum L. (green chili) cultivated under soil conditions. Increasing concentration of these trio ions significantly reduced growth parameters in a dose-dependent manner. Among them, As3⁺ exhibited the highest toxicity, completely inhibiting seed germination at 100 ppm, reduced the vigor index by 92.5%, and completely suppressed the radicle and plumule elongation. Scanning electron microscopy revealed marked deformation of root tips, while confocal microscopy indicated dose-dependent cytotoxicity in root cells. High concentrations of As3⁺ substantially reduced root and shoot biomass, chlorophyll a, chlorophyll b, carotenoids, and protein content. Conversely, stress markers such as proline, malondialdehyde (MDA), and electrolyte leakage (EL) were increased by 94%, 80%, and 68%, respectively, over control. Antioxidant enzyme activities- CAT, APX, POD, GPX, SOD, and GR in chili leaves were strongly induced at 100 ppm, indicating enhanced oxidative defense pathways. On the other hand, Cd2⁺and Cr⁶⁺ also showed toxic effects in chili plants. Metal uptake was highest at 100 ppm, with roots accumulating more Cd2⁺, Cr⁶⁺, and As3⁺ than shoots. Genotoxic analysis of root meristems revealed a sharp decline in mitotic index (MI) and multiple chromosomal aberrations, including micronuclei, stickiness, laggards, bridges, and fragments. Overall, Cd2⁺, Cr⁶⁺, and As3⁺ severely impaired plant growth, physiological responses, and genome integrity in chili, with As3⁺ exerting strong toxic effects. These findings highlight serious environmental and food-safety concerns, particularly in contaminated agricultural regions where such metals can enter the edible food chain. The results emphasize the need for mitigation strategies and field-based interventions such as microbial remediation or soil amendments to reduce heavy-metal/metalloids risks under real-world conditions.