Relevance. Eating a natural product of seedlings can completely replenish the body with missing vitamins, but there are problems in obtaining seedlings – damage to seeds by a complex of phytopathogens. Obtaining high-quality soy seedlings is an urgent task.The purpose of the research is to identify the main problems associated with the manifestation and removal of pathogenic microbiota in the production of vegetable soybean seedlings.Material and Methods. The seeds of domestic and foreign soybean varieties served as the material. Patent No. 2349098 of the Russian Federation. The determination of germination and infection of seeds was carried out according to GOST 12038-84 in 4 repetitions. Methods of disinfection of seeds: ultraviolet radiation and ozonation.Results and Discussion. It was revealed that the Hidaka variety has a high seed contamination of 48.7%, and low germination. The varieties Sibiryachka and Lydia have high germination, pathogen infestation is 6 and 8%, respectively. The contamination of the seeds of the Bar variety was a minimum of 2.7%, this variety was taken into further work. Pathogens from the genera Mucor spp., Fusarium spp., Alternaria spp., Pythium spp., Penicillium have been isolated. The phases of water consumption of vegetable soybeans have been determined, which makes it possible to determine the weight of the seed in a specific period of time and use the data for pre-sowing seed treatment. Ecological methods of disinfection of seed material have been tested – treatment with ultraviolet radiation, the use of ozone washing and ozonation of water. An analysis of the percentage of the yield of healthy and affected seedlings, depending on the method of seed treatment, showed that the untreated option has the lowest number of healthy seedlings – 10.76%. UV treatment of dry seeds and treatment in an ozone sink allowed to increase the yield of healthy seedlings to 14.24 and 14.30%, respectively. UV treatment of soaked seeds allowed to increase the yield of healthy products by 62%, and the option of using an ozone sink with further use of ozonated water allowed to obtain the maximum yield of healthy seedlings – 20.04%, which is 2 times higher relative to the control.