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Lithium-ion batteries have revolutionized portable electronics and will be a key to electrifying transport vehicles and delivering renewable electricity. Amorphous silicon (a-Si) is being intensively studied as a high-capacity anode material for next-generation lithium-ion batteries. Its lithiation has been widely thought to occur through a single-phase mechanism with gentle Li profiles, thus offering a significant potential for mitigating pulverization and capacity fade. Here, we discover a surprising two-phase process of electrochemical lithiation in a-Si by using in situ transmission electron microscopy. The lithiation occurs by the movement of a sharp phase boundary between the a-Si reactant and an amorphous Li_xSi (a-Li_xSi, x ∼ 2.5) product. Such a striking amorphous–amorphous interface exists until the remaining a-Si is consumed. Then a second step of lithiation sets in without a visible interface, resulting in the final …