The placement of the reference electrode (RE) in various bioelectrochemical systems is often varied to accommodate different reactor configurations. While the effect of the RE placement is well understood from a strictly electrochemistry perspective, there are impacts on exoelectrogenic biofilms in engineered systems that have not been adequately addressed. Varying distances between the working electrode (WE) and the RE, or the RE and the counter electrode (CE) in microbial fuel cells (MFCs) can alter bioanode characteristics. With well-spaced anode and cathode distances in an MFC, increasing the distance between the RE and anode (WE) altered bioanode cyclic voltammograms (CVs) due to the uncompensated ohmic drop. Electrochemical impedance spectra (EIS) also changed with RE distances, resulting in a calculated increase in anode resistance that varied between 17 and 31Ω (-0.2V). While WE potentials could be corrected with ohmic drop compensation during the CV tests, they could not be automatically corrected by the potentiostat in the EIS tests. The electrochemical characteristics of bioanodes were altered by their acclimation to different anode potentials that resulted from varying the distance between the RE and the CE (cathode). These differences were true changes in biofilm characteristics because the CVs were electrochemically independent of conditions resulting from changing CE to RE distances. Placing the RE outside of the current path enabled accurate bioanode characterization using CVs and EIS due to negligible ohmic resistances (0.4Ω). It is therefore concluded for bioelectrochemical systems that when possible, the RE should be placed outside the current path and near the WE, as this will result in more accurate representation of bioanode characteristics. © 2014 Wiley Periodicals, Inc.