Ukraine ranks the second (out of 123 countries) in the exports of organic products to the EU according to the study of the organic market in 2019 conducted by the Information Center Green Dossier (OrganicInfo.ua), Organic Standard and the Research Institute of Organic Agriculture (FiBL). The official statistical reviews of IFOAM confirm that in 2018 there were about 510 organic farms in Ukraine, and the total area of the agricultural land on which the organic production is carried out was 429,100 hectares. Among the producers of organic products, more than 4.6% are involved in growing of the legumes. It should be noted that one of the main crops of the Fabaceae family grown in Ukraine is soybean (Glycine max (L.) Merr.). In recent years, there has been a significant increase in sown areas and soybean production, and the issue of its organic production is relevant. The aim of our research was to determine the effect of biological products based on bacteria: Bacillus subtilis, Azotobacter, Enterobacter and Enterococcus, on the main physiological groups of soil microorganisms in the cultivation of soybean plants. The research was conducted at the Institute of Agroecology and Environmental Management of the National Academy of Agrarian Sciences of Ukraine in the Department of Agrobioresources and Ecologically Safe Technologies in the laboratory and vegetative conditions. The soybean seeds of the Suzir’ya cultivar (selected by the National Research Center of the Institute of Agriculture of the NAAS) and Kent cultivar (selected by SAATBAULINZ, Austria) were treated with biological products produced by BTU Center: Phytocide (Bacillus subtilis, cell titer 1–4·109 CFU) cm3), PhytoHelp (B. subtilis — cell titer not less than 4·109 CFU) cm3), MycoHelp (B. subtilis, Azotobacter, Enterobacter and Enterococcus) according to the recommended doses. The methods prescribed in State Standard 7847:2015 was used to determine of the soil microorganisms and their associations. Statistical data processing was performed using the Microsoft Excel software package. The peculiarities of the influence of biological products based on bacteria: Bacillus subtilis, Azotobacter, Enterobacter and Enterococcus on the main physiological groups of soil microorganisms in the cultivation of soybean plants it has been demonstrate. It has been established that in the soybean and Kent soybean agrocenosis, MycoHelp and PhytoHelp biological products effect on the main ecological and trophic groups of soil microbiome, thereby increasing soil microbiological activity; significantly intensify the development of microorganisms that use mainly organic nitrogen compounds (in the system Kent variety — biological product MycoHelp this figure increased in 3.3 times, and at the variety Constellation — biological product PhytoHelp — in 5.3 — 18.8 times compared to the reference and control options, respectively). Root exometabolites of soybean varieties determine the nature and intensity of the impact of microorganisms on plants and lead to changes in the structure of microbial groups of the rhizosphere. In the system soybean variety Kent — biological product PhytoHelp the number of oligonitrophilic bacteria is significantly reduced (by 48.7%), and in the system — soybean variety Constellation — biological products both PhytoHelp and MycoHelp — remains unchanged. By optimizing the functioning of the system, after treatment of seeds with biological products, in the soil, in the system of soybean plants of the Kent variety, the number of inactive spore forms is reduced by 2.9–5.0 times, compared to the control; the processes of organic matter destruction are weakened and its synthesis is intensified in accordance with the values of the coefficients of oligotrophic, mineralization and immobilization of nitrogen and pedotrophic. It is proved that the use of biological products MycoHelp and PhytoHelp increases the efficiency of the plant system soybean — biological products.