Two designs of benthic microbial fuel cell (BMFC) were deployed at cold seeps in Monterey Canyon, CA, unattended for between 68 and 162 days. One design had a cylindrical solid graphite anode buried vertically in sediment, and the other had a carbon fiber brush anode semi-enclosed in a chamber above the sediment–water interface. Each chamber included two check valves to allow fluid flow from the sediment into the chamber. On average, power outputs were 0.2 mW (32 mW m−2 normalized to cross sectional area) from the solid anode BMFC and from 11 to 56 mW (27–140 mW m−2) during three deployments of the chambered design. The range in power produced with the chambered BMFC was due to different valve styles, which appear to have permitted different rates of chemical seepage from the sediments into the anode chamber. Valves with the lowest breaking pressure led to the highest power production and presumably the highest inputs of electron donors. The increase in power coincided with a significant change in the microbial community associated with the anode from being dominated by epsilonproteobacteria to a more diverse community with representatives from deltaproteobacteria, epsilonproteobacteria, firmicutes, and flavobacterium/cytophaga/bacterioides (FCB). The highest levels of power delivered by the chambered BMFC would meet the energy requirements of many oceanographic sensors marketed today. In addition, these BMFCs did not exhibit signs of electrochemical passivation or progressive substrate depletion as is often observed with buried anodes.