Manuscript dataset

Soil organic carbon (SOC) sequestration in agroecosystems is crucial for mitigating climate change, yet the microbial mechanisms underlying plant diversity–driven SOC accumulation remain poorly understood. Here, we combined a multisite long-term field study with multi-omics analyses to elucidate how intercropping with woody species regulates soil carbon dynamics in tea (<i>Camellia sinensis</i>) plantations. Compared with monoculture, woody intercropping increased SOC and particulate organic carbon by 33.5% and 43.3%, respectively, primarily through enhanced litter inputs and microbial turnover. These changes were accompanied by intensified microbial nitrogen (N) limitation, a shift from copiotrophic Ascomycota to oligotrophic Basidiomycota, and an increase in N-cycling gene abundance. Enzymatic stoichiometry and network analyses revealed that N limitation stimulated resource-conservative microbial strategies and necromass formation, which promoted carbon stabilisation. Random forest modeling identified N-related factors (soil C/N ratio, total N, and leucine aminopeptidase activity) as the strongest predictors of SOC fractions. Together, our results demonstrate a dual pathway of SOC accumulation under woody intercropping—chemical inputs from lignin-rich litter and biochemical transformation via microbial necromass production. These findings highlight microbial N limitation as a key ecological mechanism linking plant diversity to belowground carbon persistence, providing a trait-based framework for optimising carbon sequestration in perennial agroforestry systems under global change.