A novel enzymatic membrane bioreactor system using the non-purified culture supernatant of whiterot fungus Trametes versicolor was developed to perform decolorization of dye wastewater. The culture supernatant was periodically obtained from fungal cultures cultivated in cost-effective natural medium, which uses blackstrap molasses typically present in food waste, by gravitational sedimentation. The model dye wastewater containing an anthraquinone type dye and the supernatant exhibiting dye decolorization activity were mixed in a continuous stirred tank membrane reactor with an ultrafiltration membrane that permitted enzyme recycling in the reactor. The results obtained from the enzymatic membrane bioreactor showed that approximately 80% of decolorization and approximately constant permeation resistance were maintained for a few days of continuous treatment. Furthermore, decolorization behaviors were well described using a combined equation based on mass balance for continuous stirred tank membrane reactor and kinetics of enzymatic decolorization of the dye.