The present critical review aims to portray the principles and theoretical foundations that have been used for the application of electrochemical impedance spectroscopy (EIS) to study electron-transfer mechanisms, mass transfer phenomena and distribution of the heterogeneous properties of microbial electrochemical systems (MXCs). Over the past eight years, the application of this method has allowed major breakthroughs, especially in the field of microbial fuel cells (MFCs); however, it is still most widely extended only to the calculation of internal resistances. The use and interpretation of EIS should greatly improve since the intrinsic knowledge of this field, and efforts and current trends in this field have already allowed its understanding based on rather meaningful physical properties and not only on fitting electrical analogues. From this perspective, the use, analysis and interpretation of EIS applied to the study of MXCs are critically examined. Together with the revision of more than 150 articles directly devoted to this topic, two examples of the correct and improved analysis of EIS data are extensively presented. The first one focuses on the use of graphical methods for improving EIS analysis and the other one concentrates on the elucidation of the constant phase element (CPE) parameters. CPEs have been introduced in equivalent circuit models, sometimes without solid justification or analysis; the effective capacitance has been obtained from CPE parameters, following an unsuitable theory for the case of microbial–electrochemical interfaces. The use of CPE is reviewed in terms of meaningful physical parameters, such as biofilm thickness. The use of a finite-diffusion element is reviewed throughout estimation of accurate values for obtaining the dimensionless numbers, Schmidt and Sherwood, in the context of a dioxygen-reducing-biocathode, under different flow-rate conditions. The use and analysis of EIS in this context are still emerging, but because of the promising potential of MXCs in renewable power generation, wastewater treatment and energy-positive biorefining, among other applications, it becomes necessary to boost our global capacities for the application of EIS—and especially its interpretation—so that we achieve a better understanding and optimization of these systems.