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However, the potential effects of different management practices on soil microbial communities remain poorly understood. This study compared two neighbouring AFS in Tom\u00e9\u2010A\u00e7u (PA, Brazil) with similar land\u2010use, size, and productivity but contrasting management: organic inputs (AGF19) vs. chemical fertilization (AGF27), alongside a native forest reference area. Soil samples were evaluated through physicochemical properties, litter composition, and amplicon sequencing (16S rRNA and ITS) across three soil depths. Despite similar soil and litter characteristics, AGF19 showed a lower abundance of phytopathogenic fungi and associations with beneficial fungal taxa as biomarkers. In contrast, AGF27 exhibited signs of a microbiota shift towards a stress\u2010related community. These findings could be partially associated with modest management changes like favouring organic inputs, influencing microbial diversity, functional guilds, and soil chemistry. Differences in management could be potentially linked with the identification of a phytopathogenic fungal taxon (e.g.,\n                    <jats:italic>Fusarium<\/jats:italic>\n                    ) as a biological marker of the community sampled in the AGF27 soil. Although different from the native forest, the results strengthen the role of AFS as a sustainable agroecological strategy. 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