In this study, atomic force microscopy based nanoindentation techniques are used to measure the in situ mechanical properties of thin film, nanometer sized amorphous-silicon nanopillars (pillar diameters of 1000 nm, 500 nm, and 200 nm) at various stages of lithiation. The pillar indentation modulus and hardness are measured ex situ as-fabricated, in situ during lithiation at two different potentials (or stages of lithiation, 50 mV and 10 mV), and in situ after delithiation at 2 V. The measured modulus of the pristine amorphous silicon nanopillars was 74.7 ± 12.1 GPa. The hardness of the pristine pillars depended on depth and the contact conditions. In general, the mechanical properties of the nanopillars decreased with increased degrees of lithiation and only partially recovered upon delithiation. The inability of the silicon to recover the as fabricated mechanical properties indicates overall degradation of the pillar during only one lithiation–delithiation cycle, which could only be directly measured in situ using the employed atomic force microscopy based technique.