This work reports the successful harvesting of energy from waste produced in a microfluidic device using a fuel cell. A miniaturized glucose air-breathing microfluidic fuel cell (ABμFFC) was designed, fabricated and tested with three different configurations according to their electrode nature: inorganic, hybrid and biofuel cell. Each ABμFFC was characterized using an ideal medium, with sterile cell culture medium, and with waste produced on a microfluidic device. The inorganic-ABμFFC exhibited the highest performance compared to the rest of the configurations. As a proof-of-concept, cancer cells were cultured on a microfluidic device and the consumed cell culture media (glucose concentration <11 mM) was used as an energy source without further treatment, into the inorganic-ABμFFC. The fuel cell generated a maximum total power of 5.2 μW, which is enough energy to power low-consumption microelectronic chips. This application demonstrates that the waste produced by microfluidic applications could be potentially scavenged to produce electrical energy. It also opens the possibility to develop truly energy self-sufficient portable devices.