Forest ecosystems have been highlighted for their carbon fixation potential in both above- and belowground compartments, especially in species-rich forests. Soil microbial communities are strongly linked to soil carbon sequestration, and it is suggested that this link is mediated by the tree community, likely due to modifications of micro-environmental conditions (i.e. micro-climate, soil quality, and biotic conditions). We further expect that these relationships will depend on the scale considered, with local (i.e., at the level of a tree species pair, TSP) and neighborhood (i.e., the surrounding trees of a TSP) scale processes influencing soil conditions. We studied soil carbon concentration and the microbial community composition of 180 TSPs along a gradient of tree species richness ranging from 1 to 16 per plot in the Chinese subtropical forest experiment (BEF-China). Tree productivity and different tree functional traits were measured at both the TSP level and neighborhood level. We tested the effects of tree productivity, functional trait identity and dissimilarity on soil carbon concentrations, and if these links were mediated by the soil microbial biomass and micro-environmental conditions. Tree productivity, together with tree functional traits, modulated micro-environmental conditions with substantial consequences for soil microbial biomass. Especially, soil microbial biomass was modified by root morphological traits at both TSP and neighborhood levels. However, the effects of the root morphological traits on microbial biomass were highly scale-dependent, with a positive effect of root morphological traits at the TSP level but a negative effect at the neighborhood level. Moreover, our analyses showed a strong positive correlation between soil microbial biomass and soil carbon concentration. We found that soil carbon concentrations increased with historical carbon concentrations, themselves strongly affected by the plot topography. However, soil carbon concentrations decreased over time. Besides, soil carbon concentration increased with tree productivity and root morphological traits at the neighborhood level. Altogether, these results imply that mechanistic studies on the drivers of microbial biomass and soil carbon sequestration need to consider the different spatial scales at which the underlying mechanisms act. Moreover, quantification of the different soil carbon pools is critical to the understanding of microbial community–soil carbon stock relationships.