Contamination by heavy metals resulting from irrigation with wastewater is an important global concern, as it can lead to crop contamination, posing serious threats to human health. Despite the advances in bioremediation of soils, sustainable strategies that use beneficial microorganisms to reduce the accumulation of heavy metals in contaminated crops remain underexplored. The aim of this study was to evaluate the potential reduction of heavy metal concentration in different structures of bean plants cultivated in soils irrigated with untreated wastewater on an agricultural land located in Hidalgo, Mexico, through the inoculation of a ubiquitous soil fungus. Bean plants were inoculated with three Trichoderma spp. and distributed across eight treatments, with an additional untreated control group, following a random full design. The percentage of root colonization and concentration of heavy metals in the leaves, pods, grains, and soil were determined. The results revealed that root colonization exceeded 75%. The treatments T. harzianum + T. asperellum and T. harzianum with 3 × 106 spores ml−1 showed the greatest decrease in Cd (64.7%) and Pb (66.1%) concentrations in the grains. T. viride with 2 × 106 spores ml−1 was the most effective treatment for copper reduction (72.9%) in grains; T. harzianum with 3 × 106 spores ml−1 showed the best performance for chromium reduction (75.7%), which was below the detection limit in leaves. In conclusion, inoculation of bean plants with Trichoderma spp. effectively reduced the accumulation of heavy metals. Future research in this area could contribute to the development of sustainable strategies to mitigate heavy metal contamination in agricultural ecosystems, thereby promoting food and environmental safety.