X-ray diffraction (XRD) and Fourier transform extended X-ray absorption fine structure (EXAFS) analysis of X-ray absorption spectroscopy (XAS) measurements have been employed to determine structural and bonding changes, as a function of the lithium content/state of charge, of germanium nanowires used as the active anode material within lithium ion batteries (LIBs). Our data, collected throughout the course of battery cycling (operando), indicate that lithium incorporation within the nanostructured germanium occurs heterogeneously, preferentially into amorphous regions over crystalline domains. Maintenance of the molecular structural integrity within the germanium nanowire is dependent on the depth of discharge. Discharging to a shallower cutoff voltage preserves partial crystallinity for several cycles.