Extracted dataset underlying a multilevel meta-analysis of the effect of intercropping on soil organic carbon (SOC) in rubber (Hevea brasiliensis) plantations. The file contained 880 paired observations from 65 peer-reviewed field studies conducted in eight countries, each comparing an intercropped system with an adjacent rubber monoculture at the same site.Each record holds the study identifier and bibliographic details, site coordinates and climate, soil classification and provenance, sampling depth, plantation age, intercropping duration, planting design, nitrogen application, and intercrop species with their growth form and legume status. Paired means, standard deviations, and replication are given for soil organic carbon and for bulk density, total nitrogen, total phosphorus, total potassium, available phosphorus, available potassium, pH, texture, and soil water content. Carbon stocks, carbon change, and accumulation rates are included, together with flags recording the source of each value (table, figure, supplementary file) and whether the variance was reported or imputed.The dataset supports effect size calculation, subgroup and meta-regression analysis, sensitivity and publication bias assessment, and is intended for reuse in quantitative syntheses of soil carbon in tropical plantation systems.