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Susceptibility to desertification in southern Europe is increasing and rehabilitation of desertification-threatened Mediterranean soils is a challenge due to the inhospitality of the environment. In particular, recovery of anthropogenic soils (mainly human-derived artefacts from housing construction and other inert materials or topsoil of terminal phase municipal landfills) cannot rely on spontaneous processes and low-cost/low-impact strategies are needed to prevent desertification. Mediterranean wild legume shrubs have great potential for soil recovery and conservation against desertification, thanks to drought resistance, and their symbiosis with N₂-fixing rhizobia and arbuscular mycorrhizal fungi. In this study double inoculated autochthonous wild legume shrubs (the genistea Spartium junceum L. and the thermopsidea Anagyris foetida L.) were used in a long-term trial to recover an anthropogenic hill in a semi-arid site of southern Italy, mainly composed of inert and human-derived artefacts. Microbial inoculants strongly enhanced plant establishment and growth on the anthropogenic soil in the greenhouse and in the field up to two years. Automated Ribosomal Intergenic Spacer Analysis (ARISA) and bacterial cultivation revealed a dramatic effect of the tripartite symbiosis on the structure of soil bacterial communities that largely overcomes plant species effect and suggests synergism of AMF with the bacterial community of the mycorhizosphere. Our results demonstrate that microsymbiont inoculation on wild legume shrubs is a promising strategy to rehabilitate anthropogenic soils in Mediterranean semi-arid regions.