The number of colony-forming units (CFU) of micromycetes in soybean seeds of Suzirya and Kent varieties, created by Filazonite technology, was determined. A significant suppression of micromycetes was found in soybean seeds of Suzirya and Kent varieties compared to the control sample. It was established that the formation of CFU micromycetes on soybean seeds of the specified varieties is influenced by seed growing technologies and climatic conditions. Depending on these factors, the number of CFU micromycetes on soybean seeds of different varieties ranged from 0.2·104 CFU/g of seed to 1.5·104 CFU/g of seed, which is almost 2.5 times less than the amount in the control sample (from 0.8·104 CFU/g to 2.7·104 CFU/g of seeds). It was established that the species of phytopathogenic micromycetes belonging to the genera Alternaria, Fusarium, and Penicillium dominate in the soybean seeds of Suzirya and Kent varieties. They are factors of biological pollution of agrophytocenoses and reduction of biosafety of products. The changes in the quality indicators of the researched varieties of soybean seeds, grown under conditions of organic production using biological technologies, were determined. Based on the results of three-year research, it was established that the indicators of the content of protein and oil in the seeds of Kent and Suzirya varieties in all variants were higher than the normative indicators specified in DSTU 4964:2008. TU. SOY. At the same time, the indicator of the mass fraction of seed moisture did not exceed the permissible norms. It was established that the biochemical composition of soybean seeds had a certain influence on the genotypes of the varieties, as well as the types of soil and the climatic conditions of the growing technology. Depending on these factors, the content of protein in the soybean seeds of the studied varieties ranges from 37.5% to 41.11%, fat from 19.02% to 21.7%, and the mass fraction of moisture from 8.8% to 11.4%.