Land use change affects the balance of organic carbon (C) reserves and the global C cycle. Microbial residues are essential constituents of stable soil organic C (SOC). However, it remains unclear how microbial residue changes over time following afforestation. In this study, 16-, 23-, 52-, and 62-year-old Mongolian pine stands and 16-year-old cropland were studied in the Horqin Sandy Land, China. We analyzed changes in SOC, amino sugar content, and microbial parameters to assess how microbial communities influence soil C transformation and preservation. The results showed that SOC storage increased with stand age in the early stage of afforestation but remained unchanged at about 1.27−1.29 kg/m² after 52 a. Moreover, there were consistent increases in amino sugars and microbial residues with increasing stand age. As stand age increased from 16 to 62 a, soil pH decreased from 6.84 to 5.71, and the concentration of total amino sugars increased from 178.53 to 509.99 mg/kg. A significant negative correlation between soil pH and the concentration of specific and total amino sugars was observed, indicating that the effects of soil acidification promote amino sugar stabilization during afforestation. In contrast to the Mongolian pine plantation of the same age, the cropland accumulated more SOC and microbial residues because of fertilizer application. Across Mongolian pine plantation with different ages, there was no significant change in calculated contribution of bacterial or fungal residues to SOC, suggesting that fungi were consistently the dominant contributors to SOC with increasing time. Our results indicate that afforestation in the Horqin Sandy Land promotes efficient microbial growth and residue accumulation in SOC stocks and has a consistent positive impact on SOC persistence.