Effluents from the textile industry have a negative environmental impact due to their high load of dyes and hard-to-remove compounds: additives, detergents, and surfactants; these must be treated before effluents can be discharged into water. White-rot fungi show great potential for the bioremediation of water and soil matrices contaminated with recalcitrant pollutants (these are generally toxic). In this work, we designed a 5 L fixed bed reactor and evaluated its performance on the degradation of pollutants in effluents from the textile industry in continuous-operation mode under non-sterile conditions, using ligninolytic fungus Bjerkandera sp. (anamorphic state R1). This setup was based on a previous design of a 0.25 L fixed-bed model bioreactor. The system was designed by taking into account the geometric and hydrodynamic similarities of both setups. In continuous-mode color-removal assays, the bioreactor was operated at a 36 h Hydraulic retention time (HRT), a 1 L/min air flux at 33 °C, and a dye concentration of 75 g/L (sulfur black 1) and 6.5 g/L (indigo Vat blue 1). 69% of the dye was removed, and changes in the chemical structures of the dyes confirmed the ligninolytic activity of the microorganism as the main dye removal mechanism.