Purpose Afforestation is increasingly recognized as an effective measure to mitigate elevated atmospheric carbon (C) dioxide and combat climate change. While afforestation can increase C sequestration by biomass production with tree growth, little is known about whether and how tree growth affects soil organic carbon (SOC) stocks and stability. Here, we aimed to explore mechanisms underlying changes in SOC stocks and fractions with stand development from the perspective of tree-microbe-mineral interactions. Methods We measured aboveground plant input, soil pH and exchangeable base cations, microbial biomass, hydrolytic and oxidative enzymes, and SOC stocks and fractions along an age-sequence of Mongolian pine (Pinus sylvestris var. mongolica) plantations with six age classes ranging from 15- to 61-year-old and adjacent grasslands in the Keerqin Sandy Lands, Northeast China. Results We found that afforestation of grasslands did not significantly affect 0-100 cm SOC stocks. Ecosystem C stocks linearly increased with stand development, and this C accretion was mainly attributed to tree biomass C sequestration. Topsoil (0-10 cm soil layer) mineral-associated C (MAOC) stocks and absolute phenol oxidase activities increased, and particulate organic C (POC) stocks and absolute beta-glucosidase activities decreased with increasing stand age, but these changes disappeared in the 61-year-old stand. Structural equation model revealed that topsoil MAOC stocks were directly related to bacterial biomass and absolute beta-glucosidase and phenol oxidase activities, and topsoil POC stocks were directly related to absolute beta-glucosidase activities. Conclusions Our findings suggest that soil microbes play a central role in mediating the dynamics of SOC stocks and stability along stand development.