Coffee (Coffea arabica) is one of the most important tropical crops in the world, and root-knot nematode (Meloidogyne spp.) infections are one of the main factors that negatively affect crop yields throughout the South American region. This study aimed to evaluate the role of indigenous arbuscular mycorrhizal fungi against root-knot nematode infections in coffee plants grown under different soil conditions in the Peruvian Amazon. The experimental design was a 3A × 2B × 4C factorial scheme with 24 treatments. Each experimental unit consisted of six coffee plants, with three replicates in randomized blocks, totaling 18 coffee plants per treatment. The studied factors were soil conditions (A), types of coffee propagation (B), and arbuscular mycorrhizal fungi consortia (C). The data were statistically examined by three-way analysis of variance, and the Tukey HSD test was applied for multiple comparisons of group means. Mycorrhiza-induced tolerance was confirmed against root-knot nematodes, as the severity of infection was significantly lower in mycorrhizal roots, with an average reduction of 52.5%, 38.5% and 38.3% in coffee plants inoculated with Huall-pache, Do-cat, and Mo-cat, respectively. Furthermore, the effects on plant growth and biological control vary depending on the diversity of arbuscular mycorrhizal fungi consortia, soil conditions, and type of propagation. This study therefore demonstrates that the inoculation of coffee plants with indigenous arbuscular mycorrhizal fungi prior to field establishment promotes coffee plant growth after root-knot nematode infections.