A new experimental setup for the characterization of flexible micro-thermoelectric generators is reported. The system can measure the power generated and the thermoelectric conversion efficiency of devices under mechanical stresses and deformations, in atmospheric environment and under vacuum, in the temperature interval 293 K-423 K, as a function of the load resistance and of the mechanical pressure, with an uncertainty on the temperature difference of ±0.02 K. The system has been tested on commercial rigid devices and on a custom-made, flexible, proof-of-concept, organic-inorganic hybrid generator made of eight thermocouples. Repeatability on the power generated and conversion efficiency within 5% and 3%, respectively, was demonstrated, and accuracy of the measurement was granted by minimization of all the potential sources of heat flux losses.