Silicon and germanium are both recognized as a promising anode material for high-energy lithium-ion batteries. Si is best known for its superior energy storage capacity, while Ge exhibits better rate capability and cycleability. To better understand the underlying reasons behind their lithiation behavior differences, particularly the enhanced Li transport in Ge, we examine and compare Li-host lattice interactions and dynamics using density functional theory calculations. At the onset of lithiation, an isolated Li interstitial is found to form polar covalent bonds with four nearest host atoms, while the degree of covalency is noticeably greater for Li–Si than Li–Ge bonds. The relatively stronger Li–Si interaction, along with the stiffer Si lattice tend to be responsible for the suppressed Li mobility (D Li = 10−13 cm2 s−1) in c-Si, as compared to the c-Ge case (D Li = 10−11 cm2 s−1). With continued lithiation, D Li in a-Li x Si increases significantly from 10−12 to 10−7 cm2 s−1 (x = 0.14–3.57); contrarily, D Li in a-Li x Ge is around 10−7 cm2 s−1 and less concentration dependent. Our analysis shows that the rapid Li diffusion in a-Li x Ge is directly related to the facile atomic rearrangements of host Ge atoms even at the early stages of lithiation.