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 (Camellia sinensis) 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.