<p>Most dyes are toxic and persistent in the environment. Therefore, the development of sustainable technologies for the treatment of dye-contaminated wastewater is imperative to mitigate water pollution. In this study, a double-chamber microbial fuel cell (MFC) integrated with a pine needle biochar-based proton exchange membrane (PSPB30) was used to decolorize and degrade the hazardous Congo red (CR) dye in simulated wastewater, resulting in the formation of less harmful metabolites. The performance of the MFC integrated with PSPB30 was evaluated at different dye concentrations (100–700 ppm), in the presence of glucose as a co-substrate, and under varying temperature conditions. The use of glucose as co-substrate improved the dye degradation from ⁓81% to 91%. Similarly, better dye degradation was observed at higher temperature. The maximum decolorization was observed at 300 ppm of CR dye in simulated wastewater. MFC inoculated with anaerobic sludge removed ~92% of color and 46% of chemical oxygen demand along with a voltage output of 245mV. The degradation of CR was confirmed by UV-visible spectrophotometer, Fourier transform infrared spectroscopy (FTIR), and gas chromatography mass spectrometry (GC-MS) analyses. The detection of several low-molecular-weight compounds, including non-toxic hydroxyl and hydroperoxy intermediates, during the treatment of CR dye wastewater confirmed the biotransformation of complex azo dye structures into environmentally safer compounds. The phytotoxicity study also confirmed that the degraded products were less toxic to the germination rate and growth of <i>Vigna radiata</i> seedlings than the untreated dye. The possible CR dye degradation pathways were also proposed. This approach is a sustainable solution for azo dye pollution owing to its simple, inexpensive MFC-P_SPB30 setup and dual benefits of wastewater treatment and renewable energy generation.</p>