In this study, the protective role of royal jelly (RJ) against the potential toxic effects of sodium benzoate was investigated in Allium cepa L. test material with physiological, genetic, and biochemical parameters. Physiological changes were evaluated by determining weight gain, rooting percentage, root length, and relative injury rate. The genetic evaluations were carried out with chromosomal abnormalities (CAs), micronucleus (MN), tail DNA formation, and mitotic index (MI) ratio parameters. The biochemical evaluations were carried out by determining lipid peroxidation and antioxidant enzyme activities by determining levels of malondialdehyde (MDA), glutathione reductase (GR), superoxide dismutase (SOD), and catalase (CAT). Further, the interaction of sodium benzoate with antioxidant enzymes was evaluated with molecular docking analysis. The antimutagenic effect of RJ was evaluated as the inhibition of chromosomal abnormalities (CAs) and tail DNA formations. A total of six groups were formed in the study. A. cepa L. bulbs in the control group were treated with tap water; the bulbs in the administration groups were treated with sodium benzoate (100 mg/L), RJ (25 mg/L and 50 mg/L doses), and sodium benzoate-RJ combinations with these doses for 72 h. As a result, it was determined that sodium benzoate application caused inhibition of physiological parameters and MI; induced MN, CAs, and DNA damage; and also caused oxidative stress. Depending on the concentration of RJ application, it reduced sodium benzoate toxicity by showing therapeutic effects in all these parameters. Also, the interaction of sodium benzoate with antioxidant enzyme residues was determined by molecular docking analysis. As a result, it has been understood that abandoning the use of sodium benzoate will be beneficial for the environment and human health and concluded that the use of RJ in the daily diet will be effective in reducing the impact of exposed toxic ingredients.