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Soil ecosystem disturbances promoted by the biological invasion can promote soil food web degradation by disrupting arbuscular mycorrhizal fungi (AMF) community structure. We aimed to compare the benefit of native tree plantings (e.g., Araucaria angustifolia, Ilex paraguariensis, and Mimosa scabrella) in a 5-year agroforestry system to overcome the soil disturbance due to invasion by Pine trees on AMF community composition in the Southern Brazil to natural restoration (unassisted forest ecosystem). We used morphological AMF identification and the natural forest as reference ecosystem. AMF diversity and dominance in the native tree species and unassisted forest ecosystem were similar, but these environments showed higher values when compared to the natural ecosystem. The PCA analysis showed soil pH, microbial biomass carbon, AMF richness, and the presence of Claroideoglomus …