Membrane separators are key elements of microbial fuel cells (MFCs), especially of those constructed in a dual-chamber configuration. Until now, membranes made of Nafion have been applied the most widely to set-up MFCs. However, there is a broader agreement in the literature that Nafion is expensive and in many cases, does not meet the actual (mainly mass transfer-specific) requirements demanded by the process and users. Driven by these issues, there has been notable progress in the development of alternative materials for membrane fabrication, among which those relying on the deployment of ionic liquids are emerging. In this review, the background of and recent advances in ionic liquid-containing separators, particularly supported ionic liquid membranes (SILMs), designed for MFC applications are addressed and evaluated. After an assessment of the basic criteria to be fulfilled by membranes in MFCs, experiences with SILMs will be outlined, along with important aspects of transport processes. Finally, a comparison with the literature is presented to elaborate on how MFCs installed with SILM perform relative to similar systems assembled with other, e.g., Nafion, membranes.