Soil organic carbon (SOC) stabilization is vital for the mitigation of global climate change and retention of soil carbon stocks. However, there are knowledge gaps on how SOC sources and stabilization respond to vegetation restoration. Therefore, we investigated lignin phenol and amino sugar biomarkers, SOC physical fractions and chemical structure in one farmland and four stands of a Robinia pseudoacacia plantation. We observed that the content of SOC increased with afforestation, but the different biomarkers had different contributions to SOC. Compared to farmland, the contribution of lignin phenols to SOC decreased in the plantations, whereas there was no difference among the four stand ages, likely resulting from the balance between increasing lignin derivation input and increasing lignin degradation. Conversely, vegetation restoration increased the content of microbial necromass carbon (MNC) and the contribution of MNC to SOC, mainly because microbial residue decomposition was inhibited by decreasing the activity of leucine aminopeptidase, while microbial necromass preservation was promoted by adjusting soil variables (soil water content, clay, pH and total nitrogen). In addition, vegetation restoration increased the particulate organic carbon (POC), mineral-associated organic carbon (MAOC) pools and the O-alkyl C intensify. Overall, vegetation restoration affected SOC composition by regulating lignin phenols and microbial necromass and also altered SOC stabilization by increasing the physically stable MAOC pool during late afforestation. The results of this study suggest that more attention should be given to SOC sequestration and stability during late vegetation restoration.