The use of biodestructors in agricultural technologies for efficient decomposition of crop residues affects the number and species composition of soil fungi, especially pathogenic species, and as a consequence, plant productivity. However, to date, this issue has not been extensively studied. The purpose of this experiment was to develop an effective method of destruction of post-harvest residues using biological products to realize the productive potential of soybeans in rice crop rotation. The work was conducted on the experimental plots of the Institute of Rice NAAS (Skadovsk district, Kherson region, Ukraine) during 2016-2018. In the experiment, the treatment of post-harvest rice residues with a biodestructor Biocomplex-BTU "Ecostern" (1 l/ha) in combination with concentrated amide water-soluble fertilizer, carbamide (30 kg/ha) was carried out in autumn. Application of carbamide alone (30 kg/ha) was used as a control. "Ecostern" is a concentrated agent, which comprises antagonists of pathogenic microorganisms as well as fungi and bacteria that accelerate decomposition of plant residues. The application of biodestructor Biocomplex-BTU "Ecostern" (1 l/ha) in combination with carbamide increased the total number of pathogenic and saprotrophic fungi in the soil from 65.5 to 80.5 thousand /g of soil or by 22.9%. However, the content of pathogenic microflora under this condition was 21.8% lower compared to the control (30 kg/ha carbamide), and the number of saprotrophs increased 3.3-fold. Following the combined use of biodestructor "Ecostern" and carbamide, the number of antagonist fungi has doubled, while the number of toxin-forming fungi decreased by 9.4%. The yield of soybeans also increased by 0.6 t/ha or by 17.9% compared to the control. The increase in yield was observed due to the higher standing density of plants and the number of beans per plant. Before the harvest, the standing density of soybean plants was 45 pcs/m 2 , which is 9.7% higher than the control (41 pcs/m 2 ), due to the high level of field germination of seeds. The number of beans was 24 and 28 pieces per plant, exceeding the control by 16.7%, and the weight of 1000 grains was 156.2 g and 157.5 g, which is 0.8% than the control.