Bioelectrochemical systems (BESs) may be used to upgrade anaerobic digester biogas by directly converting CO2 to CH4. The objective of this study was to evaluate gas (N-2, CO2, CH4, and H-2) and carbon transport within a methanogenic BES. Four BES configurations were evaluated: abiotic anode with abiotic cathode (AAn-ACa), bioanode with abiotic cathode (BAn-ACa), abiotic anode with biocathode (AAn-BCa), and bioanode with biocathode (BAn-BCa). Transport of N-2, a gas commonly used for flushing anoxic systems, out of the anode headspace ranged from 3.7 to 6.2L/d-atm-m(2), normalized to the proton exchange membrane (PEM) surface area and net driving pressure (NDP). CO2 was transported from the cathode to the anode headspace at rates from 3.7 to 5.4L/d-atm-m(2). The flux of H-2 from cathode to anode headspace was 48% greater when the system had a biocathode (AAn-BCa) than when H-2 was produced at an abiotic cathode (BAn-ACa), even though the abiotic cathode headspace had 75% more H-2 than the AAn-BCa biocathode at the end of 1 day. A 7-day carbon balance of a batch-fed BAn-BCa BES showed transient microbial carbon storage and a net transport of carbon from anode to cathode. After a 7-day batch incubation, the CH4 production in the biocathode was 27% greater on a molar basis than the initial CO2 supplied to the biocathode headspace, indicating conversion of CO2 produced in the anode. This research expands the current understanding of methanogenic BES operation, which may be used in improving the assessment of BES performance and/or in the development of alternative BES designs and mathematical models. Biotechnol. Bioeng. 2017;114: 961-969. (C) 2016 Wiley Periodicals, Inc.