The understanding of germanium Li-ion insertion/extraction reaction mechanism is drawing more and more attention in the field of Li-ion batteries. When a germanium thin film electrode is inserted with Li ions, the material remains amorphous until it crystallizes into Li15Ge4 as evidenced by X-ray diffraction. The local coordination environment of the Ge atoms of the intermediate amorphous phases was investigated by in situ X-ray absorption spectroscopy. Li-ion insertion and extraction were electrochemically controlled by continuous and intermittent galvanostatic methods. The evolution of the coordination number and interatomic distance of Ge–Ge and Ge–Li shells was determined as a function of Li composition. From a short range ordering perspective, it was observed that the first Ge–Ge interatomic distance increases and the Ge–Ge coordination number decreases with increasing Li content. The opposite is observed for the first Li–Ge interaction. Moreover, it was found that electrochemical lithiation is reversible at the atomic scale.