Soil biodiversity loss due to pollution may affect ecosystem services negatively. This environmental problem may be solved by phytoremediation, which is an effective strategy to manage and remediate contaminated areas. During this remediation process, the establishment of plant communities may improve soil fungal community structure and, in particular, may favour mycorrhizal symbiotic associations. As a consequence, afforestation of degraded lands will have different outcomes on fungal diversity and functionality, which will depend on the selected tree and shrub species. We analysed soil fungal diversity and functional guilds by high-throughput sequencing of environmental DNA in a trace element contaminated area, part of a large scale phytoremediation project running for 20 years. We selected five habitats for comparison purposes: three under the canopy of selected tree species (wild olive, white poplar and stone pine), adjacent treeless areas (grassland) and non-remediated areas (bare soil). Soil fungal diversity and richness seemed to be enhanced by phytoremediation. White poplar soil had the highest diversity and richness compared to wild olive and stone pine. Fungal communities were especially different between stone pine, with soils rich in organic C and high C:N ratio, and grassland soils. We identified 9,428 fungal OTUs from which 1,283 were assigned to a unique functional guild; the most abundant belonging to saprotrophic, plant pathogenic and ectomycorrhizal functional guilds. Ectomycorrhizal fungi were more abundant in soils under ectomycorrhizal host trees. Saprotrophs were abundant in grassland and wild olive soils, while plant pathogens were abundant in non-remediated soils. The remediation of soils (clean-up and amendment addition) allowed the natural establishment of grassland habitats throughout the study area, increasing fungal diversity, richness, taxonomy and functionality, when compared to non-remediated soils. Tree afforestation allowed the establishment of a forest type community bringing a further recruitment of fungal taxa, mainly the ectomycorrhizal fungal guild. Afforestation with different tree species showed species-specific effects on soil N, organic C, Ca and C:N ratio which led to increased spatial heterogeneity in areas with potential to recruit a wider diversity of fungi.