Microbial fuel cells (MFCs) as a technology than can convert chemical energy in wastewater into electricity has attracted increasing attentions. Improvements of the performance of MFCs are often aimed at enhancing the catalytic activity of electroactive biofilms and electrode materials. However, the electrode kinetics are also highly dependent on mass transfer processes, which can be the rate-limiting steps in the electrochemical/bioelectrochemical reactions occurring in MFCs. These transfer processes include the substrate and ion fluxes in the anode, oxygen/substrate crossover and ion fluxes across separators, as well as the oxygen and ion fluxes in the cathode. A high concentration gradient resulting from an insufficient reactant supply and product removal would lead to a concentration overpotential, which deteriorate the MFC performance. A better understanding of the transport phenomenon in MFCs could be helpful for alleviating the mass transfer limitation and could provide the guidance for electrode and MFC design, dramatically increasing the power outputs and greatly contributing to large-scale applications of MFCs. This study provides a review that firstly discusses the fundamental principles of mass transfer processes and quantitatively analyzes these processes in MFCs, analyzes and summarizes the mass transfer limitations in different components of MFCs, and finally concludes with a perspective highlighting the major challenges and possible strategies for minimizing mass transfer losses for further performance enhancement.