Novel copper-containing bionanocomposites based on the natural raw arabinogalactan have been obtained as universal effective agents against phytopathogen Clavibacter sepedonicus and development stimulants of agricultural plants. Thus, the use of such nanosystems offers a solution to the tasks set in biotechnology while maintaining high environmental standards using non-toxic, biocompatible, and biodegradable natural biopolymers. The physicochemical characteristics of nanocomposites were determined using a number of analytical methods (elemental analysis, transmission electron microscopy and spectroscopic parameters of electron paramagnetic resonance, UV–visible, etc.). The results of the study under the influence of the nanocomposites on the germination of soybean seeds (Glycine max L.) and the vegetation of potatoes (Solanum tuberosum L.) showed the best results in terms of biometric indicators. It is especially worth noting the pronounced influence of the nanocomposite on the development of the root system, and the increase in the mass of the potato root system reached 19%. It is also worth noting that the nanocomposites showed a stimulating effect on the antioxidant system and did not have a negative effect on the content of pigments in potato tissues. Moreover, the resulting bionanocomposite showed a pronounced antibacterial effect against the phytopathogenic bacterium. During the co-incubation of phytopathogen Clavibacter sepedonicus in the presence of the nanocomposite, the number of cells in the bacterial suspension decreased by up to 40% compared to that in the control, and a 10% decrease in the dehydrogenase activity of cells was also detected.