Background. In order to reduce the negative impact of mineral fertilizers and pesticides on agroecosystems, environmentally friendly plant protection systems are increasingly being utilized in soybean cultivation technologies. These systems aim to provide essential nutrients to plants while minimizing ecological harm. Materials and Methods. In vegetative studies, the processes of formation and functioning of symbiotic systems in soybeans with active strains of nodulating bacteria Bradyrhizobium japonicum (РC07, PC09, B78, B144) were investigated under the influence of pre-sowing seed treatment with the biofungicides Mycosan-N and Phytocide-r. Microbiological, physiological, statistical methods, and gas chromatography were employed in the research. Results. The impact of biological fungicides on the nodulation activity of nodule bacteria has been identified. It was determined that with comprehensive treatment of soybean seeds with B. japonicum РC07 and Mycosan-N, the mass of nodules formed on the roots exceeded that of the control plants by 7‒22 %, and under the influence of Phytocide-r, the mass was lower by 6‒20 % throughout the vegetation period. With the combined application of B. japonicum PC09 and Mycosan-N, a decrease in the number of root nodules by 8‒25 % and a reduction in their mass by 18‒35 % was observed throughout the vegetation period. Under the influence of Phytocide-r, with the inoculation of rhizobia strain PC09, the number of nodules was lower compared to the control plants only in the full flowering stage. At the same time, the reduction in their mass was 6‒20 % throughout the entire observation period. A stimulating effect of both biofungicides on the formation of the symbiotic apparatus involving strains B. japonicum B78 and B144 has been identified. With the combined application of B. japonicum РC07 and Phytocide-r, nitrogenase activity of symbiotic systems decreased by 7 % only in the stage of three true leaves compared to plants whose seeds were treated only with rhizobia. The nitrogenase activity of symbiotic systems formed with the participation of B. japonicum B78 and under the influence of Mycosan-N increased by 28 %, 15 %, and 12 % in the stages of three true leaves, budding, and full flowering, respectively. The action of Phytocide-r, with the inoculation by the nodule bacteria B78, resulted in an increase in nitrogenase activity by 14 % only in the budding stage. Under the comprehensive treatment of soybean seeds with involved biofungicides and B. japonicum B144, an increase in the intensity of N2 assimilation was noted by 29‒34 % in the stage of three true leaves and by 10‒16 % in the budding stage. Conclusions. The application of a scientifically justified selection of rhizobial strains and biological plant protection agents for pre-sowing treatment of soybean seeds will enable a more complete realization of their nitrogen-fixing potential and phytoprotective effects.