The present study focuses on ectomycorrhizal (ECM) fungi, a group of fungi that are extremely vital to the functioning of forest ecosystems. Over a three-year period, we monitored above- and belowground communities of ECM fungi in protected and managed stands located in Poland in Central European mixed forests dominated by Scots pine. Ectomycorrhizal fungi have been evaluated in three pairs of forest reserves and adjacent managed forests using a combination of classical and molecular identification methods. We found that the managed forests harbored, in total, a higher number of fungal taxa than the reserves (105 vs. 93); however, no significant difference in the average number of ECM fungal taxa was found between both management strategies (69.0 ± 6.0 vs. 61.3 ± 11.5). This was true both for sporocarps and ectomycorrhizal communities. In terms of environmental factors, soil nitrate concentration and number of trees were found to be the main drivers shaping the ECM fungal communities. The species composition of ECM fungal communities was to a large extent similar between forest reserves and managed forests, and only a small pool of species was found uniquely on one of the stand types. Species of conservation value (red-listed and rare species in Poland) have been noted on stands influenced by both management strategies. Our results suggest that both forest reserves and managed forests contribute to maintaining ECM fungal diversity, with managed forests contributing a higher total taxa pool, and each management regime contributing a certain number of taxa not found in the other.