Microbial desalination cell (MDC) can treat wastewater and saline water simultaneously and generate power. The aim of the present research work was to identify the critical factors influencing COD reduction and power generation from the MDC reactor and to optimize the control parameters. The experimental study was conducted by using medium to high-strength wastewater from distillery and brewery industry in batch-wise operation. The maximum voltage of 702 mV and current of 2.16 mA were observed for the carbon brush electrode. The mediated aeration process with the presence of potassium ferricyanide was reported in 87% COD reduction and 992 mV voltage generation. The presence of the microbial culture provided 82% COD reduction and 51% TDS reduction. The maximum current density (CD) of 0.04 mA/cm2 was observed for carbon brush, and a maximum power density (PD) of 15.56 mW/cm2 was found with aeration and potassium ferricyanide mediator. This study provided insight towards the impact of the electrode materials and the effects of mediator, aeration, and microbial culture on MDC performance.