Soil microbial communities play an important role in ecosystems functioning and are on the field scale essential for plant nutrition and health. On a larger scale, they contribute to global element cycling. Furthermore, they are involved in the turnover processes of organic matter, the breakdown of xenobiotics and the formation of soil aggregates. An ecological state of soils depends on the structure and activity of soil microorganisms. The results of soil monitoring in various ecosystems in different climatic zones of Ukraine showed a clear trend for the correlation between the agroecological conditions and activity of microbiocenosis. The most significant influence of agricultural activity on the soil microbiota can be observed on the poorly soddy-podzolic and gray forest soils, where the crop cultivation without fertilization resulted in a decrease in the total count of microorganisms by 2.2-4.5 times. Application of agricultural measures aimed at achieving maximum productivity, specifically the combination of mineral, organic and biological fertilizers, contributes to an average 1.3-4.1 times increase in the total count of microorganisms in the soil, compared with non-fertilized variants. Soils with low content of organic matter and acidic medium, soddy-podzolic and gray forest soils were characterized by a high number of micromycetes, 136-185×103 CFU·g-1 soil, and a relatively low number of eutrophic and nitrogen-fixing microorganisms. The soil of natural ecosystems is characterized by a high total count of the microorganisms with a balanced structure of various ecological-trophic groups and balanced processes of mineralization-immobilization, organic matter decomposition, and humus accumulation.