Methylene blue (MB) is a textile dye that can be fatal to aquatic life, plants, and human health when discharged into the environment without treatment. A cheese whey-microbial fuel cell (CW-MFC) is a device that generates electricity from the degradation of cheese whey by microbial activity. The microbial activity of the CW-MFC during electricity production was able to decolorize MB. In this study, 50 ppm of MB was used to evaluate the decolorization capability of bacteria of the CW-MFC. A bacterial consortium present in the bioanode of the CW-MFC showed good MB decolorization in both the ex situ and in situ operations. Ex situ operation performed outside the CW-MFC reactor showed 92.2% MB decolorization within 18 h, while the in situ operation conducted inside the CW-MFC reactor showed 97.1% MB decolorization within the same timeframe. The maximum decolorization performance was achieved at pH 4 and 37 °C. The treated MB exhibited very little or no toxicity in the germination, rooting, and shooting of Oryza sativa compared to the untreated MB. Thus, the CW-MFC can be used as a promising technique to decolorize and remove the toxic effects of MB-contaminated wastewater, and the treated wastewater can be applicable for irrigation purposes.