Macroscopic degradation of cathode materials in lithium-ion batteries often begin with microscopic changes and it is important to study pristine and cycled materials at the atomic level. Electron microscopy is widely used to characterize battery materials owing to the high spatial resolution it provides using a variety of imaging, diffraction and spectroscopy techniques. However, researchers are often faced with ambiguities in structural determination of these materials due to similarities between various phases present in battery materials and oversimplifications in interpreting the data. Furthermore, there are experimental challenges due to the electron beam-sensitive and air-sensitive nature of many battery materials. In this talk, I will discuss two examples to demonstrate challenges in structure determination. For lithium- and manganese-rich lithium transition metal oxides, I will demonstrate how atomic resolution, HAADF STEM imaging using multiple zone axes was critical in solving the structure while diffraction provided ambiguous results. For electrochemically cycled nickel-rich lithium transition metal oxides, I will show how electron diffraction, including 4D STEM nanodiffraction mapping helped in correctly identifying the transformed phase as compared to atomic resolution imaging that exhibited higher amount of ambiguity. Finally, I will discuss development of tools such as an air-free transfer in situ TEM holder, an air-free transfer module for FIB/SEM, a cryo-biasing holder and a continuous rotation tomography holder that were designed specifically to address experimental challenges in electron microscopy of air-sensitive and electron beam-sensitive materials.