LiCoO2 can experience over-lithiation (over-discharge) in an electrochemical cell due to poor battery management, failure such as a short circuit, or when LiCoO2 is utilized as a negative electrode conversion material. In order to understand the chemical and morphological changes which occur during over-lithiation, LiCoO2 electrodes were studied during deep discharge to 0.8V with operando X-ray absorption spectroscopy and spectroscopic X-ray microscopy. During over-lithiation, micron-sized LiCoO2 particles suffer significant cracking, pulverization and an incomplete conversion to Co metal. These irreversible morphological and structural changes inflict permanent damage on the cathode even during a single over-lithiation event and highlight the need for more sophisticated battery management systems.