Microbial Electrochemical Cells (MECs) technology offer a promising, integrated solution for wastewater treatment and hydrogen production. The present research aims to optimize the operation of a hybrid system for achieving high-efficiency wastewater treatment, carbon capture, and hydrogen production. Multi-criteria decision methods are used to identify optimal conditions for maximum performance. Wastewater Flow Rate (WFR), Energy Consumption (EC), Nanocomposites Concentration (NC), and Temperature (T) are chosen as input parameters. Utilizing the Entropy-TOPSIS (Technique for Order of Preference by Similarity to Ideal Solution) method, the optimal outputs were determined for specific input settings. The proposed system exhibited optimal input settings at 1100 m³/day (WFR), 95 kW (EC), 34 mg/L (NC), and 36 °C (T). NC emerged as the most influential parameter, holding a significance weightage of 32%, followed closely by temperature. Under these optimized conditions, the system demonstrated exceptional performance, achieving a Wastewater Treatment Efficiency of 98.1%, Carbon Capture Efficiency of 97%, and a Hydrogen production flow rate of 17.76 m³/hr. This research lays a foundation for sustainable and versatile wastewater management practices, emphasizing the potential of MEC systems in contributing to cleaner and resource-efficient industrial ecosystems.