The field of energy storage and conversion materials has witnessed transformative advancements owing to the integration of advanced in situ characterization techniques. Among them, numerous real-time characterization techniques, especially in situ transmission electron microscopy (TEM)/scanning TEM (STEM) have tremendously increased the atomic-level understanding of the minute transition states in energy materials during electrochemical processes. Advanced forms of in situ/operando TEM and STEM microscopic techniques also provide incredible insights into material phenomena at the finest scale and aid to monitor phase transformations and degradation mechanisms in lithium-ion batteries. Notably, the solid–electrolyte interface (SEI) is one the most significant factors that associated with the performance of rechargeable batteries. The SEI critically controls the electrochemical reactions occur at the electrode–electrolyte interface. Intricate chemical reactions in energy materials interfaces can be effectively monitored using temperature-sensitive in situ STEM techniques, deciphering the reaction mechanisms prevailing in the degradation pathways of energy materials with nano- to micrometer-scale spatial resolution. Further, the advent of cryogenic (Cryo)-TEM has enhanced these studies by preserving the native state of sensitive materials. Cryo-TEM also allows the observation of metastable phases and reaction intermediates that are otherwise challenging to capture. Along with these sophisticated techniques, Focused ion beam (FIB) induction has also been instrumental in preparing site-specific cross-sectional samples, facilitating the high-resolution analysis of interfaces and layers within energy devices. The holistic integration of these advanced characterization techniques provides a comprehensive understanding of the dynamic changes in energy materials. This review highlights the recent progress in employing state-of-the-art characterization techniques such as in situ TEM, STEM, Cryo-TEM, and FIB for detailed investigation into the structural and chemical dynamics of energy storage and conversion materials.