Abstract A microbial fuel cell (MFC) is a bioinspired energy converter which directly converts biomass into electricity through the catalytic activity of a specific species of bacteria. The effect of temperature on a miniaturized microbial fuel cell with Geobacter sulfurreducens dominated mixed inoculum is investigated in this paper for the first time. The miniaturized MFC warrants investigation due to its small thermal mass, and a customized setup is built for the temperature effect characterization. The experiment demonstrates that the optimal temperature for the miniaturized MFC is 322–326 K (49–53 °C). When the temperature is increased from 294 to 322 K, a remarkable current density improvement of 282% is observed, from 2.2 to 6.2 Am−2. Furthermore, we perform in depth analysis on the effect of temperature on the miniaturized MFC, and found that the activation energy for the current limiting mechanism of the MFC is approximately between 0.132 and 0.146 eV, and the result suggest that the electron transfer between cytochrome c is the limiting process for the miniaturized MFC.