The present study aimed at exploring to explore the penoxsulam toxicity and protective effects of blueberry extract in roots of Allium cepa L. The effective concentration (EC50) of penoxsulam was determined at 20 µg/L by the root growth inhibition test as the concentration reducing the root length by 50%. The bulbs of A. cepa L. were treated with tap water, blueberry extracts (25 and 50 mg/L), penoxsulam (20 µg/L) and combination of blueberry extracts (25 and 50 mg/L) with penoxsulam (20 µg/L) for 96 h. The results revealed that penoxsulam exposure inhibited cell division, rooting percentage, growth rate, root length and weight gain in the roots of A. cepa L. In addition, it induced chromosomal anomalies such as sticky chromosome, fragment, unequal distribution of chromatin, bridge, vagrant chromosome and c-mitosis and DNA strand breaks. Further, penoxsulam treatment enhanced malondialdehyde content and SOD, CAT and GR antioxidant enzyme activities. Molecular docking results supported the up-regulation of antioxidant enzyme SOD, CAT and GR. Against all these toxicity, blueberry extracts reduced penoxsulam toxicity in a concentration-dependent manner. The highest amount of recovery for cytological, morphological and oxidative stress parameters was observed when using blueberry extract at a concentration of 50 mg/L. In addition, blueberry extracts application showed a positive correlation with weight gain, root length, mitotic index and rooting percentage whereas a negative correlation with micronucleus formation, DNA damage, chromosomal aberrations, antioxidant enzymes activities and lipid peroxidation indicating its protecting effects. As a result, it has been seen that the blueberry extract can tolerate all these toxic effects of penoxsulam depending on the concentration, and it has been understood that it is a good protective natural product against such chemical exposures.