Batteries can store energy from alternative, intermittent sources via chemical reactions for later use in electronics, transportation, and grid load leveling. Most commercial rechargeable batteries are based on lithium ion intercalation into layered metal oxides, the mechanism of which is fairly well understood. To move forward in the development of novel electrode materials versus lithium, deeper insight into heretofore unexplored methods of charge storage must be gained. X-ray diffraction (XRD) and X-ray absorption spectroscopy (XAS) are invaluable techniques for studying the atomic structure of molecules, materials, and systems relevant to electrochemical energy storage. The broad purpose of this dissertation work is to observe and understand the structural changes that occur within materials that are cycled electrochemically in a lithium-ion battery (LIB). A specially designed coin cell allows for the investigation of chemical changes as observed with X-rays within the LIB as a function of the state of charge. This cell design has been used to study germanium nanowire anodes and anthraquinone-based cathodes at the Cornell High Energy Synchrotron Source (CHESS). The fully assembled coin cell is aligned in the beamline and connected to a galvanostat. Powder X-ray diffraction patterns or X-ray absorption spectra are then collected at regular intervals as lithium ions enter and leave the structure under operating battery conditions. The resultant data give insight to the complexity of the mechanisms of solid-state interactions with lithium ions, and the following chapters will expand upon this. Briefly, germanium nanowires lithiate heterogeneously, preferentially into amorphous regions, and their crystalline cores can be maintained for a few cycles if the voltage cutoff limit is kept above 0.3V vs. Li/Li+. Also, for the organic cathodes, reversible crystallographic changes are observed that demonstrate that structural reorganization occurs to accommodate the coordination of positive charge within a reduced molecular crystal. The original contribution to knowledge from this body of work is that crystalline domains need not be maintained in an electrochemically stable system. These and other in-depth mechanistic operando studies presented herein provide a unique view of dynamic battery systems and guide future investigations.