Microbial desalination cell (MDC) is a bioelectrochemical system developed recently from microbial fuel cells (MFCs), for producing green energy from organic wastes along with desalination of saltwater. MDC is proved to be a better performer than MFC in terms of power output and chemical oxygen demand removal, with desalination as an additional feature. This study investigates the application potential of MDC for integrated biodegradation of waste engine oil. This study showed, for the first time, that waste engine oil could be used as an organic substrate in MDC, achieving biodegradation of engine oil along with considerable desalination and power production. Utilization of these wastes in MDC can protect the environment from waste engine oil contamination. Indigenous oil-degrading bacteria were isolated and identified from engine oil contaminated sludge. Degradation of waste engine oil by these novel isolates was studied in batch cultures and optimized the growth conditions. The same cultures when used in MDC, gave enhanced biodegradation (70.1±0.5% ) along with desalination (68.3±0.6% ) and power production (3.1±0.3 mW/m²). Fourier transform-infrared spectroscopy and gas chromatography-mass spectrometry analyses were performed to characterize the degradation metabolites in the anolyte of MDC which clearly indicated the biodegradation of long chain, branched and cyclic hydrocarbons present in waste engine oil.