Microbial electrolysis cells (MECs) are perceived as a potential and promising innovative biotechnological tool that can convert carbon-rich waste biomass or wastewater into hydrogen (H2) or other value-added chemicals. Undesired methane (CH4) producing H2 sinks, including methanogens, is a serious challenge faced by MECs to achieve high-rate H2 production. Methanogens can consume H2 to produce CH4 in MECs, which has led to a drop of H2 production efficiency, H2 production rate (HPR) and also a low percentage of H2 in the produced biogas. Organized inference related to the interactions of microbes and potential processes has assisted in understanding approaches and concepts for inhibiting the growth of methanogens and profitable scale up design. Thus, here in we review the current developments and also the improvements constituted for the reduction of microbial H2 losses to methanogens. Firstly, the greatest challenge in achieving practical applications of MECs; undesirable microorganisms (methanogens) growth and various studied techniques for eliminating and reducing methanogens activities in MECs were discussed. Additionally, this extensive review also considers prospects for stimulating future research that could help to achieve more information and would provide the focus and path towards MECs as well as their possibilities for simultaneously generating H2 and waste remediation.