Synthesis of zinc oxide nanoparticles (ZnO-NPs) via green method is an outstanding alternative to conventional/ regular methods; however, the safety or toxicity of the biosynthesized ZnO-NPs in vivo is not fully explored. This study was conducted to evaluate the protective efficiency of cinnamaldehyde-loaded chitosan nanoparticles (Cin@CSNPs) against oxidative damage and genotoxicity of ZnO-NPs in mice. ZnO-NPs were biosynthesized using the extract of fresh leaves of Mentha pulegium L. Cin was extracted from cinnamon essential oil, and was loaded into chitosan nanoparticle (Cin@CSNPs). Both ZnO-NPs, Cin@CSNPs and CSNPs were characterized. The in vitro release of Cin@CSNPs was determined. In the biological study, 6 groups of male BALB/c mice were treated by gavage for 3 weeks as follows, control group, the group received ZnO-NPs (25 mg/kg b.w), the groups received Cin@CSNPs at low dose (50 mg/kg b.w) or high dose (100 mg/kg b.w), and the groups received ZnO-NPs plus Cin@CSNPs at the 2 tested doses. Blood and tissue samples were collected for different biochemical, genetical and histological studies. The particle size of ZnO-NPs, CSNPs, and Cin@CSNPs were (20.78 ± 2.60), (170.0 ± 3.7), and (218.23 ± 2.90) nm, and ξ-potential were (32.7 ± 4.6), (8.32 ± 0.27) and (4.80 ± 0.21) mV, respectively. ZnO-NPs disturbed the biochemical and oxidative stress indices, AFP, CEA, TNF-α, chromosomal aberrations in somatic and germ cells, and sperm abnormality along with severe pathological changes in the hepatic, renal, and testicular tissues. Cin@CSNPs improved significantly all the parameters tested and the histological picture in a dose-dependent. Therefore, the biosynthesized ZnO-NPs exhibit oxidative damage and genotoxicity, and Cin@CSNPs have potential protective effects against the risks of ZnO-NPs and may be a promising tool to overcome the challenges of using Cin in food and pharmaceuticals applications.