In this study, the toxic effects of 1,4-dioxane, a common contaminant, and the protective property of Ceratonia siliqua L. pod extract (Cspe) against this toxicity are aimed to be demonstrated with a versatile model. For this purpose, Allium toxicity test was used and six different experimental groups were formed. While the control group was germinated in tap water, the application groups were germinated in mediums containing 750 mg/L Cspe, 1500 mg/L Cspe, 100 mg/L 1,4-dioxane, 750 mg/L Cspe+100 mg/L 1,4-dioxane, and 1500 mg/L Cspe+100 mg/L 1,4-dioxane. Each group was germinated in related solution for 72 h and alterations in physiological, biochemical, genetic, and anatomical parameters were investigated. Germination percentage, relative injury rate, root length, and weight gain parameters were examined as physiological parameters, and no significant difference was observed in the control group and only-Cspe-treated groups. In groups treated with 100 mg/L 1,4-dioxane, germination percentage, root length, and weight gain were significantly decreased, and the relative injury rate reached the highest value as 0.48. It was determined that all physiological parameters improved in the groups where Cspe and 1,4-dioxane treated together, and the relative injury rate decreased to 0.22 in the group treated with 1500 mg/L Cspe+1,4-dioxane. Genotoxic effects were tested by the micronucleus and chromosomal abnormality frequency, and statistically insignificant micronucleus formation was found in control group and Cspe-treated groups. Micronucleus frequency were found to be 58.00 ± 12.12 and 31.00 ± 07.38 in 1,4-dioxane and 1500 mg/L Cspe+1,4-dioxane-treated groups, respectively. This result showed that the application of 1500 mg/L Cspe had a 46.5% reduction in the frequency of 1,4-dioxane-induced micronucleus and had a protective effect on genomic integrity. It has been found that 1,4-dioxane application induces lipid peroxidation and increases malondialdehyde level 4.5 times compared with control group. Oxidative stress, which was proved by increased malondialdehyde levels in 1,4-dioxane-treated group caused induction of superoxide dismutase and catalase enzymes, and it was determined that enzyme activities increased by 1.99 and 4.9 times, respectively, compared with the control group. Cspe treatment with 1,4-dioxane caused a significant decrease in malondialdehyde level, superoxide dismutase, and catalase enzyme activities, indicating that oxidative stress formation in the cells was repressed. Abnormalities such as cell deformation, cell wall thickening, and flattened cell nuclei were seen in 1,4-dioxane-treated group in the cross sections of root tips, and the frequency of these abnormalities decreased with Cspe application. As a result, it was determined that 1,4-dioxane caused a versatile toxicity in the test material Allium cepa, whereas Cspe application had a dose-dependent protective feature against toxicity in all tested parameters.