A consortium of fungal isolates may improve phytoremediation by stimulating root growth whereas biochar reduces metal leaching in contaminated soils. We combined these treatments to evaluate to what extent Jacaranda mimosifolia D. Don seedlings extract metals (Cu, Mn, and Zn) and reduce leaching in soil columns. Contamination treatments were established by combining Cu (200 mg dm−3), Mn (450 mg dm−3), and Zn (450 mg dm−3). A spore suspension of five fungal isolates (Beauveria bassiana, Metarhizium anisopliae, Pochonia chlamydosporia, Purpureocillium lilacinum, and Trichoderma asperella) was sprayed on plant shoots and the soil surface. Biochar (1% m/v) was produced by the pyrolysis of wood sawdust and applied to the soil surface. Finally, control treatments were established in a completely randomized block design. The consortium of fungal isolates increased shoot and root mass, improved the translocation potential of Cu (translocation factor (TF) of 0.25), Mn (TF of 2.93), and Zn (TF of 1.79) from roots to shoots, and increased the total accumulated mass of Mn and Zn in shoots and roots. Biochar applications improved Cu, Mn, and Zn translocation and increased the total accumulated mass of shoot Mn. Moreover, a combination of fungal isolates and biochar increased the translocation factor to 0.44 for Cu, 1.70 for Mn, and 1.34 for Zn relative to the treatment with J. mimosifolia in contaminated soil (CJ); increased shoot Cu concentration; and reduced total leached Cu by a factor of 22.9, Mn by 5.5, and Zn by 22.9 relative to the CJ treatment. A photochemical profile, based on chlorophyll a fluorescence, showed that Jacaranda mimosifolia was tolerant to contaminated soil and is a potential phytoremediator of Cu, Mn, and Zn. Overall, the consortium of fungal isolates and biochar improved the efficiency of phytoremediation by concentrating metals in plant tissue and reducing the risks of leaching.