The structural transformations of silicon nanowires when cycled against lithium were evaluated using electrochemical potential spectroscopy and galvanostatic cycling. During the charge, the nanowires alloy with lithium to form an amorphous Li x Si compound. At potentials <50mV, a structural transformation occurs. In studies on micron-sized particles previously reported in the literature, this transformation is a crystallization to a metastable Li15Si4 phase. X-ray diffraction measurements on the Si nanowires, however, show that they are amorphous, suggesting that a different amorphous phase (Li y Si) is formed. Lithium is removed from this phase in the discharge to form amorphous silicon. We have found that limiting the voltage in the charge to 70mV results in improved efficiency and cyclability compared to charging to 10mV. This improvement is due to the suppression of the transformation at low potentials, which alloys for reversible cycling of amorphous silicon nanowires.