The atomistic mechanisms during lithiation and delithiation of amorphous Si nanowires (a-SiNW) have been investigated over cycles by molecular dynamics simulations. First, the modified embedded atom method potential from Cui et al. [J. Power Sources 207, 150 (2012).] has been further optimized on static (LixSi alloy phases and point-defect energies) and on dynamic properties (Li diffusion) to reproduce the lithiation of small crystalline Si nanowires calculated at the ab initio level. The lithiation of a-SiNW reveals a two-phase process of lithiation with a larger diffusion interface compared to crystalline Si lithiation. Compressive axial stresses are observed in the amorphous SixLi alloy outer shell. They are easily released thanks to the soft glassy behavior of the amorphous alloy. Conversely, in crystalline SiNW, the larger stress in the narrow crystalline lithiated interface is hardly released and requires a phase transformation to amorphous to operate, which delays the lithiation. The history of the charge-discharge cycles as well as the temperature appear as driving forces for phase transformation from amorphous LixSi alloy to the more stable crystalline phase counterpart. Our work suggests that a SiNW anode with an enhanced plastic behavior could help release the internal stress, while a full delithiation could heal the cracks that appear with time and thus increase the life cycles of Li-ion batteries using such anode materials.