Microbial desalination cell (MDC) is a type of bioelectrochemical reactors that integrates microbial fuel cell (MFC) process for wastewater treatment with electrodialysis process for desalinating saline water while recovering electricity. Microbial-based technologies produce electricity by utilizing the organic waste found in wastewater as a substrate through a microbial catalyzed electrochemical reaction. This creates a potential gradient between the anode and the cathode that stimulates the ions' transfer through an ion-exchange membrane. Microbial electrolysis cell (MEC) works in the same principle of MDC. Unlike the conventional MFC, it lacks a terminal acceptor of the electrons that results in the production of hydrogen at the cathode compartment. This chapter discussed the current progress of MDC in terms of treating different types of wastewater, while desalinating seawater, removing different pollutants, and generating electricity. Moreover, it provided the available integrated technologies for the production of biohydrogen, biomethane, and other fuels using a MEC. In addition, current challenges from these technologies were highlighted. Finally, it provided an effective future perspective for overcoming these challenges and paths for success.