The article presents the results of a study of the microbial cenosis of typical slightly eroded chernozem under crops of corn for grain and oats under conditions of the use of agrobiotechnologies, including the treatment of seeds, soil, plants and post-harvest residues with microbiological preparations based on Trichoderma and Lactobacillus, as well as the use of nitrogen fertilizers and lime against the background of surface incorporation by-products. The research was carried out on the territory of the Federal State Budgetary Institution “Kursk FATS” (Medvensky district, Kursky district, Panino village) in two fields. In 2022, in the first field (grain crop rotation) oats (Avena sativa L.) variety “Borets” (predecessor – buckwheat) were cultivated, in the second (grain crop rotation) – hybrid corn (Zea mays L.) variety “Delitop” ( predecessor – winter wheat). The soil of the experimental field is typical low-humus, slightly eroded, heavy loamy chernozem on carbonate loess-like loam. It was established that during the harvesting phase under corn and oats, regardless of the factors (microbiological preparations, nitrogen fertilizers and lime) of the experiment, the soil was characterized by an increase in the number of saprophytic microflora and micromycetes compared to the phase of crop germination. The introduction of microbiological preparations based on Trichoderma and Lactobacillus with nitrogen fertilizers and by-products contributed to an increase in soil biogenicity, which on average during the growing season exceeded the control by 43.9 and 57.2%, respectively, under corn and oats. The maximum number of microscopic fungi was noted with the combined use of Trichoplant, SK and Biogor-Zh with mineral nitrogen, but the soil under oats in terms of the content of fungal microflora was 8.9 thousand CFU/g soils exceeded their amount under corn crops. The highest value of the transformation coefficient of organic matter was observed when by-products were inoculated with microbiological preparations with lime, regardless of the culture and timing of determination (phases of germination and harvesting of crops).