Intrinsic soil properties have been shown to mediate the effects of ectomycorrhizal (ECM) fungi and their associated trees on soil organic matter (SOM) and nitrogen (N) cycling, but variation in the contribution of fungal communities to ECM effects across different forests remains uncertain. To investigate the potential role of fungal communities in driving observed variation in ECM effects, we characterized fungal community composition and function using DNA sequence variability of the ITS2 region of the fungal rRNA operon and measured chemical properties of forest floor leaf litter, soil organic horizon, and soil mineral horizons (0–5cm, 15–20 cm depth) beneath ECM-associated Oreomunnea mexicana focal trees. We sampled beneath focal trees in arbuscular mycorrhizal (AM)- and ECM-dominated stands within four adjacent watersheds that differed in underlying soil pH and fertility. We found that overall fungal community composition and the ratio of ECM to saprotrophic fungi differed between AM- and ECM-dominated stands in the lowest pH and fertility watershed but were similar between stand mycorrhizal types in the highest pH and fertility watershed. Patterns in fungal community composition and function aligned with patterns in N isotopic composition of forest floor leaf litter and mineral soil, which could reflect greater ECM transfer of N to the trees and greater contribution of hyphal biomass to SOM in the lowest pH and fertility watershed. Overall, our results suggest the potential for watershed-scale variation in soil pH and fertility to mediate fungal community contributions to variation in ECM effects on biogeochemical syndromes.