This talk gives an overview of the PI’s research program on the opportunities and challenges of in situ transmission electron microscopy (TEM) to study novel two dimensional materials and metal oxides for Li-ion and Na-ion battery applications. Various anode materials including SnO2, ZnSb, MnO2 , phosphorene were subjected to lithiation process and the transport of Li ions was visualized within their atomic structure. For SnO2 nanowires, it was observed that the Li ion transport results in local strain development preferably along (200) or (020) plans and [001] crystallographic directions. Extremely fast ionic transport was also observed along [100] directions of phosphorene and in ZnSb crystalline materials indicating that atomic structure engineering of electrode materials can provide an efficient path for the movement of larger ions such as sodium ions overcoming their sluggish kinetics. In one-dimensional materials the structural engineering of tunnels and the tunnel stabilizers can be very effective in allowing the ions to be transported at fast rates. Overall a summary will be given on new science obtained from the in situ TEM studies and how this new information can help to further grow the opportunities in materials designed for electrochemistry.