The development of eco-friendly thin-film thermoelectric generators for microenergy harvesting applications is highly desired. Ge-based materials have recently attracted significant research interest because of their superior performance at room temperature as human-compatible thermoelectric constituents. We examined the synthesis of Yb3Ge5 thin films and assessed their thermoelectric properties, considering the exceptional ability of Yb as a heavy metal to scatter phonons. The components of the resulting thin film were strongly dependent on the Yb/Ge deposition ratio and the subsequent annealing temperature. An increase in the Yb content augmented the formation of Yb2O3, whereas an increase in the Ge content facilitated the formation of Ge crystals. These trends were more evident at higher annealing temperatures. By controlling the YbGe composition, a power factor of 1470 µW m−1 K−2 was obtained at an annealing temperature of 700 °C, along with a low thermal conductivity of 3.1 W m−1 K−1. Machine-learning-facilitated data analysis revealed that the high power factor originated from Yb3Ge5. Notably, the power factor reached 1370 µW m−1 K−2 even at a temperature of 500 °C, causing the expansion of heat-resistant plastic films. Thus, we established the impressive potential of Yb3Ge5 as a suitable material for eco-friendly thin-film thermoelectric generators.