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Abstract Graphene oxide (GO) synthesised by modified Tour’s method was decorated with copper and zinc nanoparticles (NPs) and simultaneously reduced by sodium borohydride to obtain a nanocomposite of reduced GO with copper and zinc NPs (rGO–Cu–Zn). The nanocomposite rGO–Cu–Zn was characterised by transmission electron microscopy (TEM), energy dispersive X-ray (EDX) spectroscopy, X-ray diffraction (XRD) and X-ray photoelectron spectroscopy (XPS). The rGO–Cu–Zn was tested against Xanthomonas euvesicatoria (X. euvesicatoria), which attacks tomatoes and causes bacterial spots (BSs), and compared with the commercial product Champion 50 WG. Total bacterial growth inhibition was observed for the 1% rGO–Cu–Zn, whereas Champion 50 WG at the same concentration inhibited but did not eradicate all the bacterial colonies. To evaluate the negative effect of the rGO–Cu–Zn on the molecular level, the expression of the genes associated with the action of abiotic and biotic stress factors was analysed. Gene expression in the plants treated with 10% rGO–Cu–Zn did not exhibit a noticeable increase. Graphical Abstract