Understanding mechanisms of deformation of battery cell components is important in order to improve the mechanical safety of lithium-ion batteries. In this study, micro-scale deformation and failure of fully-discharged battery components including an anode, a cathode, and a separator were investigated at room temperature. Nanoindentation tests and in-situ tensile tests under scanning electron microscope (SEM) were carried out on the electrodes of a commercial battery cell in order to measure the elastic modulus of coating materials and the elastic–plastic and fracture behavior of the electrodes. Additionally, interrupted tests were conducted on a polypropylene separator and its deformation at each stage was investigated under SEM. Samples with the same size were loaded to different strains and then fully unloaded. SEM and X-ray diffraction (XRD) techniques were subsequently used to analyze the changes in the microstructure such as crystal orientation and pore size. From these tests, it was found that cathode and anode coatings have distinct deformation mechanisms. The cathode develops a number of micro cracks on the surface before reaching final failure, while the anode maintains its integrity until later stages of deformation. The separator also shows unique stages of deformation such as elongation of fibrils and formation of new pores until reaching final onset of failure.