This article reviews the use of micro-organisms as catalysts at the electrodes of microbial fuel cells (MFCs). The principle of MFCs and their intended use for water treatment and clean electricity production is discussed. We address the different microbial structure and metabolic pathways found in prokaryote (bacteria) and eukaryote (yeasts) that allow the understanding of why electron transfer is possible between a microbe and an electrode. The different mechanisms of microbe–electrode electron transfer are discussed: direct electron transfer or through natural nanowires (pili), mediated electron transfer by natural or artificial redox mediator and finally direct redox transformation of excreted metabolites at the electrodes. This is followed by a review of the different bacteria that have been found and studied in MFCs mainly in the anodic compartment but also more recently in the cathodic side of the fuel cells. A perspective on the possible advantages and challenges of the use of yeasts in MFCs is provided, as this aspect has not been thoroughly studied so far. The fourth section of the review focuses on how to improve the performance and sustainability of MFCs through the functionalisation of the electrode surface, for instance with the covalent grafting of redox mediators and/or enzymes.