As the Earth's biota enters the sixth great mass extinction event recorded in the history of the planet, it is predicted that the erosion of biodiversity will result in the reduction of the goods and services that ecosystems provide. To mediate the loss of biodiversity and ecosystem function associated with wood production in temperate forests in Europe, a near-to-nature strategy has been developed. Whether this strategy enables natural assembly mechanisms of fungi responsible for major ecosystem processes is unknown.We analysed variation in species richness and both the functional and phylogenetic structure of fungal assemblages of different trophic life histories (soil saprotrophic, wood saprotrophic, and ectomycorrhizal fungi) in 69 beech forest plots along a steep gradient of management intensity. We focused on reproductive traits to test the hypothesis that management intensity shifts community assembly mechanisms from limitations in niche overlap that promote the coexistence of dissimilar species to environmental filtering that selects for similar species. Specifically, we hypothesized that unpredictable resources in production forests filter the assemblages, promoting species with small fruit bodies and with small and elongated spores.As management intensity increased, functional diversity decreased from a random pattern to a clustered pattern, which indicated that management intensity increased the strength of environmental filtering. However, phylogenetic diversity increased from a random pattern to an over-dispersed pattern. Combining phylogenetic diversity with functional diversity did not provide additional insight into the traits but revealed a contrasting pattern. Reproduction traits of the assemblages shifted, with a decrease in mean fruit body size and an increase in spore elongation.Synthesis and applications. Near-to-nature logging concepts are not able to mimic the major processes that shape fungal community assembly in protected forests. This could have severe consequences for important ecosystem functions provided by fungi. The phylogenetic over-dispersion indicated that analyses of other traits in addition to reproductive traits are required to disentangle the factors affecting fungal community structure.This article is protected by copyright. All rights reserved.