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Abstract Background Salvadora persica is an endangered medicinal plant due to difficulties in its traditional propagation. It is rich in bioactive compounds that possess many pharmaceutical, antimicrobial activities and widely used in folk medicine. The current study aims at in vitro propagation of Salvadora persica and the application of different nanoparticles (NPs) to induce the synthesis of bioactive and secondary metabolites within the plant. The cellular and genetic responses to the application of different NPs were evaluated. Results The impact of nanoparticles NPs (ZnO, SiO2, and Fe3O4) on callus growth of Salvadora persica and the production of its active constituent benzyl isothiocyanate was examined, regarding some oxidative stress markers, antioxidant enzymes, and genetic variabilities. An encouraging impact of 0.5 mg/l ZnO NPs on benzyl isothiocyanate production was shown reaching up to 0.905 mg/g callus fresh weight in comparison to 0.539 mg/g in control callus. This was associated with decreasing hydrogen peroxide content and increasing superoxide dismutase and peroxidase activities. The deposition of the NPs on cellular organelles was detected using a transmission microscope. Fifteen Inter-Simple Sequence Repeats (ISSR) primers detected an overall, 79.1% polymorphism among different treatments. A reduction in genomic DNA template stability (GTS) was made and was more pronounced in higher doses of different NPs. Conclusion This study is a stepping stone in developing a productive protocol for in vitro production of benzyl isothiocyanate from Salvadora persica using NPs as a valuable anticancer compound.