A fuel cell sensor was demonstrated as a low cost on-line monitoring tool for hydrogen producing microbial electrolysis cells (MECs) at lab scale. Hydrogen produced in the MEC was oxidized at the anode of the fuel cell generating electricity that could be easily monitored. The total electrical current obtained was proved to correlate with the hydrogen supplied (r2 0.99) and was equally efficient as other reference analytical methodologies based on gas chromatography. Signal was repeatable (2.3% variation coefficient, n=12) and did not show interferences by the presence of other compounds like methane and carbon dioxide. The fuel cell was coupled to single and double chamber MECs validating its applicability as on-line monitoring portable device for quantifying hydrogen production. The use of the fuel cell as an on-line hydrogen sensor offers an alternative to more complex methodologies and offers the possibility to implement control systems and optimization strategies.