Biodiversity has been elucidated to be one of the major factors sustaining ecosystem functioning. The vast majority of studies showing a relationship between biodiversity and ecosystem functioning have come from experiments, and this knowledge has not yet been applied to most real-world cases of conservation and management. This is especially true in forest ecosystems, characterized by the dominance of long-lived organisms (trees) and high levels of structural complexity and environmental heterogeneity. To apply biodiversity–function relationships to actual forest management, there are several issues to be considered. These include employing a cross-taxon perspective, as some functions (e.g. soil biogeochemical processes) cannot be maintained by a narrow set of organisms, as is usually the case with experimental systems. More specifically, although the interaction between above- and below-ground diversity is important for many functions in forests, there are few studies that evaluated the roles of diversity in both subsystems in a manner that could be informative in practice. To evaluate the roles of above- and below-ground diversity to support natural soil ecosystem functions, we conducted a decomposition experiment in the northern forests of Japan, which are currently under restoration management. The restoration area consists of mosaics of different vegetation types by various revegetation activities and establishment of ungulate exclosures. Using structural equation modelling and linear mixed-effects models, we assessed direct and indirect pathways from diversity to functions by focusing on both of taxonomic and functional diversity indices. To put our findings into practice, we utilized a trait-based approach, which provides a link between the functional consequences of human influences and ecosystem structure. We found little direct effects of tree diversity on below-ground functions such as decomposition rate and litter stabilization. However, once the diversities of understorey herbaceous plants and soil fungi were considered as a possible mediating explanatory factor, we found a significant effect of tree diversity to indirectly support these functions by supporting these other types of biodiversity. Particularly, we found that the models based on functional trait diversity, rather than on taxonomic species richness, best explained the variation in below-ground processes. Synthesis and applications. Forest restoration in the northern forests of Japan has had no explicit objective to restore soil functions. Nevertheless, afforestation, and the associated increase in tree diversity as a measure of forest restoration, was, although often unintentionally, proven effective for the maintenance of multiple ecosystem functions, such as soil biogeochemical processes. This finding suggests a great potential for management to make local tree assemblages functionally dissimilar and diverse for the sake of supporting and enhancing fundamental ecosystem functions in forests.