Membranes serve as a fundamental component in microbial fuel cell (MFC) configurations, particularly in the context of real wastewater treatment. Although proton exchange membranes (PEMs) are traditionally employed, increasing attention has been directed toward ion-selective alternatives such as anion exchange membranes (AEMs) and cation exchange membranes due to their distinct ion transport mechanisms and potential cost advantages. This study investigates the comparative performance of anion exchange membranes (AEMs), cation exchange membranes (CEMs) and bipolar membranes (BPMs) in dual-chamber MFCs operated under fed-batch real wastewater conditions. Experimental studies focused on electrical output, pH shifts, changes in chemical oxygen demand (COD), total nitrogen, phosphorus, and ammonia concentrations. The results revealed distinct performance profiles for each membrane type. The CEM system supported high removal of COD, TN, and ammonia (≈75–85% ± 2%). In contrast, the AEM achieved excellent phosphorus removal (≈95% ± 2%) alongside strong COD reduction, although nitrogen and ammonia removal were comparatively lower. BPM systems exhibited lower COD removal (typically <65%) but achieved moderate and stable reductions in TN, ammonia, and phosphorus, while producing electrical output consistently higher than AEM and at intermediate levels relative to CEM. Quantitative analysis of power generation further confirmed this trend, with CEM delivering the highest output (8.93 mW/m²), BPM providing moderate performance (3.38 mW/m²), and AEM producing the lowest (1.5 mW/m²). The results emphasize that membrane influences the balance between nutrient removal and energy recovery, and that aligning membrane selection with specific treatment objectives may advance MFCs from laboratory demonstrations toward practical applications.