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Forestry practices such as afforestation of former agricultural lands and early forest thinning are applied in several countries. These management strategies increase wood production potential and expand forest areas. However, knowledge of the impact of these practices on the diversity and resilience of soil fungal communities is scarce. This study investigated soil fungal community composition of young (21–40 years-old) Norway spruce (Picea abies (L.) Karst.) dominated stands located in Latvia and Estonia. The study includes data from 62 sampling sites and 2480 soil cores. Fungal internal transcribed spacer amplicons (ITS1-5.8S-ITS2 rDNA region) of DNA extracted from forest floor and fine soil fractions were sequenced using the PacBio sequencing platform. 3176 quality filtered OTUs were detected, and 73.9% of these were identified as fungi. Fungal community composition was mainly differentiated based on soil pH and sampling site. Regarding former land use, relative abundance of the genus Solicoccozyma was higher in samples from former agricultural sites and some species from genera Cortinarius and Russula were identified as more indicative of particular former land use. Litter saprotrophic fungi and fungi of the genus Thelephora were significantly more highly represented in unmanaged sites than in sites where thinning was performed. In conclusion, differences among soil fungal communities are mainly influenced by soil pH and sampling site. Former land use and management have a significant effect on specific genera of ectomycorrhizal and saprotrophic fungi. [ABSTRACT FROM AUTHOR]