The application of preparations of biological origin in the protection system of soybean grown under conditions of intensive irrigated crop rotations conforms to the modern tendencies of science and production development. The use of them contributes to solving ecological, production and social-economic problems. The study presents the three-year research on the efficiency of systems protecting soybean from pests and diseases based on biological and chemical preparations. The research was conducted in typical soil and climate conditions of the South of Ukraine. Zonal agricultural methods and generally accepted research methodology were used. The purpose of the research was to create a soybean protection system based on preparations of biological origin, ensuring high productivity of high-quality products reducing a negative impact of the crop production on the environment. The study emphasizes that, under irrigated conditions of the South of Ukraine, the application of biological preparations has a positive impact on the indexes of growth, development and formation of the elements of soybean yield structure. There was an increase in the crop biological weight by 13.8 % and 22.1 % and the number of seeds per plant rose by 11.6 and 14.6 % as a consequence of eliminating harmful organisms with the plant protection systems. The larger ground mass was formed by medium-ripe varieties Danai and Svyatogor, on which the increase from protection measures was higher. Weight 1000 pcs. the seeds did not undergo significant changes. It is established that the larger seeds were formed by Danaya and Svyatogor varieties, in which the average weight is 1000 pcs. seeds were 142 and 136 g, respectively, while in the variety Diona this figure was 133 g. There was an increase in the height of the lowest pod when the total plant height rose. For medium-ripe varieties was characterized by a higher attachment of beans, where the highest values of this indicator acquired in the variety Svyatogor. The medium maturing soybean variety Danaia formed the maximum yield of 3.23 and 3.35 t/ha respectively, when biological and chemical protection systems were applied. The research establishes that the application of the bio-fungicide Psevdobakterin 2 (2.0 l/ha) in the crop protection system at the beginning of soybean flowering and the bio-fungicide Baktofit (2.5 l/ha) with the bio-insecticide Lepidotsid-BTU (10.0 l/ha) at the beginning of pod formation does not reduce the productivity of the soybean varieties under study considerably, when compared to the application of chemical preparations. The research determines that the soybean protection system under study ensures a decrease in the coefficient of soybean water uptake by 7.2-13.0 %, increasing the total water intake to an inconsiderable degree. Biologization of the soybean crop protection system leads to a reduction in production costs compared to the chemical protection system. Taking into account the needs for the collection of additional products, costs increase by an average of 1 thousand UAH/ha, while for chemical protection systems by 1.8 thousand UAH/ha. At the same time, the cost is reduced by 220-360 UAH/t and the profitability of growing crops is increased by 3.8-7.8 %. There has been a reduction in the burden of pesticides on the environment and the production of cleaner products. This indicates the prospect of using the biofungicides Pseudobacterin 2 and Bactophyte and the bioinsecticide Lepidocid-BTU on soybeans to protect plants from pests.