The structure and function of plant-associated fungal communities (i.e. mycobiome) is shaped by biotic and abiotic factors, and can impact plant community dynamics. We evaluated the effects of different environmental factors in structuring the communities of seedling-associated fungi in temperate tree species, considering both the Janzen-Connell hypothesis as well as the impacts of climate warming. We tested the hypothesis that fungal host-specialization is observed at both the individual fungus and fungal community levels and is modulated by environmental conditions. The seedling fungal communities were characterized from tree species grown in two forests, under experimental manipulation of light, warming, and distance to and density of conspecifics. Fungal communities were analyzed using generalized joint attribute models. While warming, light, and forest site played a role in structuring seedling fungal communities, host, distance to, and density of conspecifics were stronger contributors. Furthermore, we could identify which fungal taxa responded to which predictors. This work supports the concept of fungal host-specialization at the community level, and points to particular fungal taxa which may play roles in density- and distance-dependent regulation of plant species diversity in the studied forests.