Abstract Background Forest restoration has been considered an effective method to increase soil organic carbon (SOC), whereas it remains unclear whether long-term forest restoration will continuously increase SOC. Such large uncertainties may be mainly due to the limited knowledge on how soil microorganisms will contribute to SOC accumulation over time. Methods We simultaneously documented SOC, total phospholipid fatty acids (PLFAs), and amino sugars (AS) content across a forest restoration gradient with average stand ages of 14, 49, 70, and > 90 years in southern China. Results The SOC and AS continuously increased with stand age. The ratio of fungal PLFAs to bacterial PLFAs showed no change with stand age, while the ratio of fungal AS to bacterial AS significantly increased. The total microbial residue-carbon (AS-C) accounted for 0.95–1.66 % in SOC across all forest restoration stages, with significantly higher in fungal residue-C (0.68–1.19 %) than bacterial residue-C (0.05–0.11 %). Furthermore, the contribution of total AS-C to SOC was positively correlated with clay content at 0–10 cm soil layer but negatively related to clay content at 10–20 cm soil layer. Conclusions These findings highlight the significant contribution of AS-C to SOC accumulation along forest restoration stages, with divergent contributions from fungal residues and bacterial residues. Soil clay content with stand age significantly affects the divergent contributions of AS-C to SOC at two different soil layers.