Microbial electrolysis cells (MECs) are an emerging technology capable of harvesting part of the potential chemical energy in organic compounds while producing hydrogen. One of the main obstacles in MECs is the bacterial anode, which usually contains mixed cultures. Non-exoelectrogens can act as a physical barrier by settling on the anode surface and displacing the exoelectrogenic microorganisms. Those non-exoelectrogens can also compete with the exoelectrogenic microorganisms for nutrients and reduce hydrogen production. In addition, the bacterial anode needs to withstand the shear and friction forces existing in domestic wastewater plants. In this study, a bacterial anode was encapsulated by a microfiltration membrane. The novel encapsulation technology is based on a small bioreactor platform (SBP) recently developed for achieving successful bioaugmentation in wastewater treatment plants. The 3D capsule (2.5 cm in length, 0.8 cm in diameter) physically separates the exoelectrogenic biofilm on the carbon cloth anode material from the natural microorganisms in the wastewater, while enabling the diffusion of nutrients through the capsule membrane. MECs based on the SBP anode (MEC-SBPs) and the MECs based on a nonencapsulated anode (MEC control) were fed with Geobacter medium supplied with acetate for 32 days, and then with artificial wastewater for another 46 days. The electrochemical activity, chemical oxygen demand (COD), bacterial anode viability and relative distribution on the MEC-SBP anode were compared with the MEC control. When the MECs were fed with artificial wastewater, the MEC-SBP produced (at −0.6 V) 1.70 ± 0.22 A m−2, twice that of the MEC control. The hydrogen evolution rates were 0.017 and 0.005 m3 m−3 day−1, respectively. The COD consumption rate for both was about the same at 650 ± 70 mg L−1. We assume that developing the encapsulated bacterial anode using the SBP technology will help overcome the problem of contamination by non-exoelectrogenic bacteria, as well as the shear and friction forces in wastewater plants.