We investigated soil fungal community composition and diversity across silvicultural treatments in a Hungarian temperate oak-hornbeam forest over two years, focusing on key functional groups: ectomycorrhizal, saprotrophic, pathogenic, and mycoparasitic fungi. Soil samples were collected from all 30 plots of the Pilis Forestry Systems Experiment in autumn 2020 and 2021, six and seven years post-treatment. High-throughput DNA metabarcoding combined with multivariate analyses assigned fungal sequences to taxonomic and functional groups. Richness and community composition were compared among treatments and between years using ANOVA for alpha diversity, and NMDS with PERANOVA for beta diversity. Silvicultural treatments significantly affected community composition in all fungal guilds (R² = 8.97–15.37%, p < 0.001). Ectomycorrhizal fungi showed reduced richness in clear-cut plots, with smaller reductions in preparation and retention treatments. Saprotrophs were more diverse in clear-cut plots but declined the following year, while plant pathogens, wood decomposers, and mycoparasites exhibited elevated richness in clear-cut treatments (p < 0.01). Root endophytes and animal parasites remained relatively stable. Community composition variation correlated with microclimatic factors such as soil temperature and moisture (R² = 6.23–12.67%, p < 0.01), altered by forest structural changes. Inter-annual comparisons revealed temporal shifts, with functional guilds showing differential successional trajectories under drier conditions in 2021. Indicator species analysis identified taxa associated with specific management regimes, including ectomycorrhizal genera (Inocybe, Russula) in control treatments, and saprotrophs and pathogens in clear-cut plots. The study documents dominant genus responses to silvicultural intensity and microclimatic gradients, providing insights for potential bioindicator use in temperate forest management.