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Forest restoration has become one of the most important challenges for restoration ecology in the recent years. In this regard, soil fungi are fundamental drivers of forest ecosystem processes, with significant implications for plant growth and survival. However, the post-disturbance recovery of belowground communities has been rarely assessed, especially in highly degraded systems such as mines. Our aim was to compare forests and mined systems for biomass and structure of fungal communities in soil during early stages of tree establishment after disturbance. We performed ergosterol analysis and PacBio and Illumina sequencing of internal transcribed spacer 2 amplicons across soil layers in <i>P. sylvestris</i>, <i>Q. robur</i> and <i>Q. ilex</i> (holm oak) forests and naturally revegetated mined sites. In pine forests, total fungal biomass was significantly higher in litter and humus compared to mineral layers, with dominance of the mycorrhizal genera <i>Tomentella</i>, <i>Inocybe</i> and <i>Tricholoma</i>. Conversely, in oak forests the most abundant mycorrhizal genera were <i>Tomentella</i>, <i>Cortinarius</i> and <i>Sebacina</i>, but the biomass of saprotrophic fungi was greater in the litter layer compared to mycorrhizal fungi, with the genus <i>Preussia</i> being the most abundant. In the revegetated mined sites, ectomycorrhizal fungi dominated in the humus and mineral layers, with the mycorrhizal genus <i>Oidiodendron</i> being dominant. In contrast, in holm oak forests saprotrophic fungi dominated both soil humus and mineral layers, with the genera of <i>Alternaria</i>, <i>Bovista</i> and <i>Mycena</i> dominating the soil humus forest layer, while the genus <i>Cadophora</i> dominated the mineral layer. The habitat-specific differences in soil fungal community composition and putative functions suggest that an understanding of soil–plant–microbial interactions for different tree species and use of specific soil/litter inoculum upon planting/seeding might help to increase the effectiveness of tree restoration strategies in Mediterranean degraded sites.