Abstract <p>The studies were conducted in 2011–2022 to improve the methods of in vitro treatment of garden crops from harmful viruses by increasing the efficiency of treatment and environmental safety. Salicylic acid at a concentration of 3 × 10^–4 M was used as an antiviral drug in the nutrient medium. Microcuttings at the stage of micropropagation itself for the purpose of treatment from viruses and increasing the reproduction rate, as well as at the rooting stage to increase rooting and improve root development, were treated using the SMI-5 model device for magnetic pulse treatment with magnetic induction pulses with a changing increasing frequency from 0.8 to 51.2 Hz for 10 min with a step of 0.2 Hz. When improving the clonal rootstocks of apple and pear trees, the use of salicylic acid made it possible to increase the yield of explants of apple rootstocks free from latent viruses by 11.8–23.7% and of pear rootstocks by 38.4–40% depending on the type of virus. A low index of latent virus content is observed during complex therapy of apple rootstock explants using salicylic acid and thermo- and magnetic therapy. Magnetic treatment contributed to the improvement of the vegetative development of explants at the propagation stage: the number of shoots increased by 1.6–1.7 times depending on the culture. At the rooting stage, in microshoots of the studied crops treated with magnetic induction pulses, significant stimulation of rhizogenesis and an increase in the number and length of roots were observed. When planting microplants in nonsterile conditions, magnetic treatment led to an improvement in their survival rate by 8–13% depending on the crop. The advantages of magnetic processing include the absence of phytotoxicity, versatility, higher yield of healthy plants, automation, and environmental safety of the processing process.</p>