This study aimed to assess the changes in chemical properties and fungal communities in the upper mineral soil layer in managed Scots pine (Pinus sylvestris L.) ecosystems. Study sites were located in the three largest P. sylvestris massifs in Lithuania, and six sampling sites, representing different development stages of the P. sylvestris forest ecosystem, were selected in each of them: mature P. sylvestris forest stands; clear-cuts of former P. sylvestris mature stand; and the P. sylvestris plantations aging from the 1st to 4th year. High-throughput sequencing was performed to evaluate the soil fungus community at clear-cuts, early-stage reforested sites, and mature forests in Lithuania. This study has shown that, among other chemical soil parameters, the mean concentrations of mineral nitrogen (N), total phosphorus (P), and P2O5 were slightly higher in the clear-cut sites, and significantly higher in the 1st year plantations compared to the mature forests. The quality filtering after PacBio sequencing showed the presence of 60,898 high-quality fungal sequences, and 1143 fungal operational taxonomic units (OTUs). The most abundant fungal OTU in our study was Archaeorhizomyces sp. 5425_1. In total, 70 mycorrhizal fungal OTUs were found in the soil samples at the studied sites. The most abundant ectomycorrhizal fungus identified was Amanita fulva (Schaeff.) Fr. The highest amount of ectomycorrhizal fungal OTUs was found in the clear-cut sites and in the mature forests. The concentrations of mineral N and P2O5 in the upper mineral soil layer did not significantly affect fungal OTUs diversity. Conversely, a relatively strong correlation was obtained between the number of mycorrhizal fungal OTUs and the concentrations of total N and soil organic carbon (SOC), as well as between the numbers of saprotrophic fungal OTUs and the concentration of magnesium ions (Mg2+).