The objective of our studies was to evaluate the effects of three plant residue management practices on the size and activity of soil microbial community and their contribution to water-stable aggregation in two agricultural soils under continuous spring barley growing. These practices included: straw harvesting, straw incorporation into a depth of 0-20 cm, and straw burning with subsequent incorporation of ash into the depth of 0-20 cm. The straw incorporation treatment, as compared to the two other ones, contributed to an insignificantly higher total amount of water-stable aggregates (0.25-10 mm) in the degraded loam Chernozem (54.14.7%) and the clayey loam Gleyic Fluvisol (62.10.7%). There were differences in the effects of the treatments on size distributions of fractions of water-stable aggregates in both soils. Among the studied treatments, the straw incorporation one led to a significantly (p = 0.01) higher increase in basal respiration only in the degraded loam Chernozem. Compared to the straw incorporation and harvesting treatment, the straw burning one had a significantly (p < 0.01) higher contribution to the accumulation of microbial biomass carbon in water-stable aggregates of the degraded loam Chernozem and the clayey loam Gleyic Fluvisol.