The aim of research is to determine the parameters of biological activity of meadow-chernozem soil and its phytoimmunity in grain-fallow crop rotation at different levels of cultivation intensification and the use of chemicals. The studies were carried out in a long-term (launched in 1973) stationary experiment in grain-fallow crop rotation (fallow – wheat – peas – wheat – barley) under pea crop in the Federal State Budgetary Scientific Institution Omsk Agrarian Scientific Center. In certain periods of 2022 and 2023, with favorable soil moisture, the presence of a significant amount of plant residues in the variant with minimum-zero tillage and the use of complex chemicals, the number of soil micromycetes and nodule bacteria increased to 93.0 thousand and 13.9 million CFU/g, respectively. The total number of soil microflora in the arable layer under different soil cultivation systems for peas without the use of complex chemicals was 51.4–61.2 million CFU/g with a difference of 19.0 % in the ascending series: No-till < moldboard < combined. The use of mineral fertilizers in combination with plant protection products in moldboard and combined tillage did not have a significant effect on the amount of soil microflora, a slight decrease to 17.0 % within the experimental error was noted. In the variants with No-till tillage in combination with intensification products, stimulation of the growth of the number of microorganisms to 22.0 % in relation to the control was noted. On average, according to the soil tillage factor, the greatest development of pea root rot was observed in the No-till variant (3.8 %), a slight decrease (3.2–3.6 %) – in moldboard and combined tillage. The use of plant protection products during the growing season of peas made it possible to reduce the development of root rot by 47.0 % relative to the control, depending on the soil tillage method. With combined treatment, the greatest prevalence of pea root system disease was noted (37.8 %), the least – with No-till treatment (30.8 %). In laboratory conditions, using the wet chamber method, a complex of root rot pathogens was determined, among which fungi of the genus Fusarium spp. prevailed.