The presence of aggregates of various sizes in the soil is an important condition for soil carbon sequestration. In this system, microbial biomass 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, microbial activity and eco-physiological indices (qCO 2 , QR, MB-SIR/SOС and qCO 2 /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 soil of crop rotation, high mineralization activity and MB-SIR were found in the aggregates 0.5-0.1 mm, in the monoculture soil in aggregates <0.1 mm and in the control soil in the 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 was determined by large aggregates (>5 mm), while in the control soil, by the aggregates 5-1 mm. Depending on the type of site and the size of aggregates, the differences in microbial metabolism were revealed. The qCO 2 and QR values decreased, and the MB-SIR/SOС and qCO 2 /SOС increased in the series: control soil > crop rotation > monoculture. In the control soil, the values of the ecophysiological indices decreased with decreasing aggregate size. And vice versa, in agricultural soils, these parameters were the highest in the microaggregates (<0.25 mm). The monoculture soil, in contrast to the control soil and crop rotation soil, turned out to be more energy efficient.