Abstract Soil microorganisms play a key role in soil organic matter (SOM) dynamics, but little is known about the controls affecting the distribution of microbial biomass and their residues in soil. Here, a forested Cambisol topsoil was incubated with 13C-labeled glycine or beech leaves for 12 weeks prior to sequential density fractionation. The incorporation of the 13C label in amino sugars (AS) was used to gain insight into bacterial and fungal assimilation of the substrates. AS derived from glycine or leaves were compared to total AS to investigate how microbial residues and active communities were distributed among soil density fractions. Bacteria slightly dominated leaf C assimilation, while a pronounced fungal dominance was observed for glycine. The glycine-derived AS and original AS were similarly distributed among the soil density fractions, both peaking in microbial aggregates (1.8–2.4 g cm−3). Leaf-derived AS were mostly found in association with the plant debris (<1.65 g cm−3). The ratios of substrate-derived AS C to substrate-derived C increased with soil fraction density for both glycine and leaves. The same pattern was observed with original AS C to soil fraction C ratios. We concluded that bacteria and fungi were most active where the resource was even though their residues accumulate mostly in microbial aggregates (1.8–2.4 g cm−3). We suggest that such accumulation might be attributed to (1) an increasing stabilization efficiency of microbial residues and (2) the progressive SOM transfer, from plant debris to microbial aggregates (1.8–2.4 g cm−3).