Understanding soil organic matter dynamics is essential for evaluation of the carbon (C) sequestration potential of soils, a critical factor in mitigating climate change. However, the dynamics of soil C processes under the canopy of extrafloral nectary (EFN) trees that are widely distributed in subtropical forests remain poorly explored, particularly in the context of declining tree diversity. In this study, we investigated EFN tree effects on the soil C and nitrogen (N) fractions in forest communities characterized by five levels of tree species richness (TSR, i.e. one-, two-, four-, eight- and 16-tree species). Emphasis was placed on the roles of the phyllosphere and soil functional fungal guilds associated with the target and neighbouring trees. The results revealed that the proportion of EFN trees negatively affected the C content of particulate organic matter (POM), the C/N ratios of the POM and mineral-associated organic matter (MAOM), as well as the POM-to-MAOM ratio. The peak soil C/N ratios across all fractions, as well as the POM-to-MAOM ratio, shifted from four-tree species to eight-tree species under the canopy of EFN trees and their neighbouring non-EFN trees. The POM C/N ratio was directly associated with the alpha diversity of soil functional fungi and indirectly associated with the alpha diversity of functional fungi colonizing damaged leaves. In addition, the C/N ratios of the POM and MAOM, and the POM-to-MAOM ratio were potentially mediated by the complexity, stability and potential keystone taxa of fungal co-occurrence networks colonizing leaves and in the soil. The changes in microbial communities are likely driven by the interaction between EFN trees and herbivorous insects. Synthesis. These findings demonstrate a positive response of soil C sequestration under extrafloral nectary (EFN) tree canopies. By highlighting the significance of EFN tree–phyllosphere/soil fungi associations and their role in shaping the effect of tree species diversity, this study contributes to a comprehensive understanding of the mechanisms by which above-ground–below-ground synergies govern soil C sequestration in a subtropical forest.