The fate of hydrophilic, hydrophobic, and insoluble fractions extracted from 13C-labelled maize straw and their use for the formation of bacterial and fungal-derived amino sugars (AS) were monitored during a 40-day incubation of upland and paddy soils. The highest sequestration of C in the AS pool was present in the hydrophilic fraction in both soils (1.1–1.4% of input C). Bacterial community in upland soil utilized the hydrophilic fraction the most for the formation of AS, whereas fungi used the hydrophobic fraction, suggesting that bacteria and fungi have different substrate preference. In contrast, fungi used similar portions of all fractions for AS formation in the paddy soil, which could be a substrate utilization strategy under anoxic conditions. Sequestration of microbial-derived C, formed from the added fractions, was lower in paddy than in upland soils (0.7–1.1% vs. 1.2–1.4%), while total AS content showed the opposite trend (493–509 mg kg−1 in paddy vs. 387–405 mg kg−1 in upland soils). This was attributed to the 1.5 times lower microbial activity in paddy than in upland soils based on the relative incorporation of 13C into total MBC. Thus, sequestration of microbial-derived C from various organic C sources is closely related to substrate quality, but soil management and its properties modulate the microbial utilization of substances with various hydrophobicity. [ABSTRACT FROM AUTHOR]