This study was focused on the application of an aerobic biofiltration (BF) with Ficus benjamina wood chips as support medium, inoculated with two basidiomycete fungi, Phanerochaete chrysosporium (BF 1) and Trametes versicolor (BF 2), to treat Tequila vinasses from a Tequila industry. The biofiltration system was compared with a biofilter system without basidiomycete fungi (BF W), in order to determine the influence of fungi on the treatment of vinasses. Three different vinasses/water ratios (30/70, 40/60, and 50/50) were evaluated. The maximum removals of chemical oxygen demand (COD) obtained during each operation step were 72% (BF 1), 72% (BF 2), and 8% (BF W) for 30 vinasses/70 water; 72% (BF 1), 73% (BF 2), and 66% (BF W) for 40 vinasses/60 water; and 22% (BF 1), 20% (BF 2), and 18% (BF W) for 50 vinasses/50 water. The total organic carbon (TOC) removal was significantly increased using a volumetric organic load of 5.5 kg COD m−3d−1. During the operation of the biofilters, the enzymatic activity of laccase was present, even at the step of highest concentration of vinasses.