The increased requirement of potable water led to the development of efficient desalination technologies such as reverse osmosis membranes, which are currently mass-manufactured. However, other approaches are being explored, as emerging countries contribute to the global demand for drinking water. Microbial desalination cells (MDC), in which microbial consortia use chemical energy to remove ions from low-salinity aqueous solutions, have been investigated for some time but the actual relevance of this technology in the overall desalination industry remains unclear. pH maintenance on the cathodic side, internal resistance along with membrane fouling and its longevity are some technical shortcomings related to the practical use of MDCs, which can be partially circumvented by using multiple interconnected configurations. Further research is required to scale up the MDC technology while decreasing its cost and environmental impact. This review summarizes the operative principle of MDCs, the most common MDC cells configurations, and describes the variables that influence their performance in light of full-scale applications. A techno-economic analysis and lifecycle assessment of microbial desalination systems is also included, along with the description of electrode fabrication and genetic manipulation strategies that can improve the MDC cells performance.