Abstract: This study aimed to enhance the conductivity and biocompatibility of microbial fuel cell (MFC) anodes to improve their performance in treating dye wastewater. Traditional carbon felt (CF) anodes were modified with polypyrrole (PPy), polyaniline (PANI), and sodium alginate (SA). The modified carbon felt anodes, PPy-SA/CF and PPy-PANI-SA/CF, were prepared via in situ polymerization. The morphological and structural characteristics of the electrodes, as well as their electricity generation performance and pollutant removal efficiency, were evaluated. Characterization of electrode morphological structures revealed that the PPy-SA/CF surface exhibited an uneven, stacked structure with higher surface roughness and wrinkle density than those of the PPy-PANI-SA/CF and CF electrodes. Electrochemical performance tests indicated that the PPy-SA/CF electrode had the lowest charge transfer resistance (32.02 Ω) and the smallest Tafel slope (28.293 V/dec), resulting in the highest specific capacitance (3 796.35 mF/cm²). These results demonstrated that the modification with PPy and SA improved the electron transfer efficiency and energy storage capacity of the CF anode. An H-type two-chamber MFC was constructed using the PPy-SA/CF anode (PPy-SA/CF-MFC) for treating methylene blue (MB) wastewater. The PPy-SA/CF-MFC exhibited superior performance, with a maximum power density ((127.14±7.26)mW/m²) and MB decolorization rate (95.15%±1.82%). These values were higher than those of PPy-PANI-SA/CF-MFC ((113.75±5.89)mW/m², 88.95%±3.91%) and CF-MFC ((57.6±5.88)mW/m², 76.15%±2.30%). The analysis of microbial community structure revealed that the anode surface of PPy-SA/CF developed a microbial community dominated by functional genera such as Syntrophomonas (3.8%) and Anaerolinea (6.3%), which exhibited significant species dominance. This dominant microbial community is identified as the primary factor responsible for the enhanced electricity generation and MB wastewater decolorization efficiency of the PPy-SA/CF-MFC.