The influence of ground lichens Flavocetraria cucullata and Certraria laevigata on chemical, biochemical and microbiological characteristics of permafrost soils of Central Yakutia was studied. It was revealed that the values of the content of organic carbon, exchangeable cations and anions, and pH did not depend on the presence or absence of lichens on the soil surface. It was revealed that the main secondary metabolites of F. cucullata were usnic, lichesteric, protolichesteric and allo-protolichesteric acids, and C. laevigata - fumarprotocetraric acid. Chromatographic analysis of soils revealed the presence of only usnic acid in humus samples under F. cucullata and adjacent areas without vegetation. It was shown that as F. cucullata moved away from the place of growth, there was a decrease in the content of usnic acid and an increase in the content of specific compounds that could be biomarkers of fungi in the soil. Analysis of fungi and bacteria in soils, performed using the cultural approach, showed an abundance of fast-growing micromycetes and bacteria. According to the metagenomic analysis, the taxonomic diversity of fungi in soils was incomparably higher than according to the cultural studies, and mycorrhizal basidiomycetes were the predominant ecological group. Ectomycorrhizal basidiomycetes are primarily susceptible to the effect of lichen F. cucullata. The allelopathic effect of C. laevigata on the soil microbiome is much less pronounced. It is assumed that usnic acid synthesized by F. cucullata diffusely spreads and accumulates in the soil, selectively suppressing the growth of ectomycorrhizal basidiomycetes.