Boreal forests carry out functions that are critical to global biogeochemical cycling and climate regulation. Soil microbial diversity has been reported to drive multiple functions simultaneously (multifunctionality) in drylands and temperate ecosystems, however, the role and importance of bacterial and fungal diversity in driving multiple soil functions in boreal forest ecosystems remains poorly understood. We collected soils from 58 plots across upland and lowland (swamp) habitats in a boreal forest ecosystem to evaluate the linkages between fungal/bacterial diversity and multiple soil functions. Fungal and bacterial diversity were determined using 18S rDNA and 16S rDNA amplicons sequencing, and functions related to nutrient cycling (dissolved inorganic and organic nitrogen and carbon, nitrification) and climate regulation (CO2 and N2O emissions) were measured. The results showed that fungal but not bacterial richness was positively related to soil multifunctionality. We further used structural equation modelling to identify the effects of fungal and bacterial communities, and other environmental variables (moisture, pH, soil organic carbon and habitat types) on multifunctionality. Our model predicted 65.0% of the variation in soil multifunctionality, and confirmed that along with moisture and habitats, fungal richness and community composition were significantly and positively associated with multifunctionality. Finally, we identified specific fungal genera strongly associated with soil multifunctionality, and saprotrophic fungi were especially important for maintaining multiple soil functions. Our results suggest that potential losses in fungal diversity could result in reductions in soil functions particularly linked to nutrient cycling and climate regulation in boreal forests.