Аннотация:The presence of aggregates of various sizes in the soil is an important condition for soil carbon sequestration. Microbial biomass in this system is a key link. This work was devoted to the study of the influence of land use systems on the distribution of SOС, MB‐SIR, its activity, and eco‐physiological indices (qCO2, QR, MB‐SIR/SOС, qCO2/SOС) in relation to the size of soil aggregates. The distribution of SOС, MB‐SIR, and mineralization activity among the aggregates was heterogeneous. In the soils of crop rotation, high mineralization activity and MB‐SIR were found in aggregates 0.5–0.1 mm, in monoculture soils in aggregates <0.1 mm, and in control soil in aggregates 1–0.25 mm. There was a general trend towards a decrease in microbial activity, MB‐SIR, and SOС availability with an increase in aggregate size. In agricultural soils, microbial activity is determined by aggregates > 5 mm; in control soils, by aggregates 5–1 mm. Differences in microbial metabolism were revealed depending on the type of site and the size of aggregates. The qCO2 and QR values decreased, and the MB‐SIR/SOС and qCO2/SOС increased in the series from control soil > crop rotation > monoculture. In the control soil, the values of the eco‐physiological indices decreased with decreasing aggregate size. And vice versa, in agricultural soils, these parameters were the highest in microaggregates (< 0.25 mm). Monoculture soils, in contrast to control soils and crop rotation soils, turned out to be more energy efficient.