Two-dimensional (2D) materials offer distinct advantages for electrochemical energy storage (EES) compared to bulk materials, including a high surface-to-volume ratio, tunable interlayer spacing, and excellent in-plane conductivity, making them highly attractive for applications in batteries and supercapacitors. Gaining a fundamental understanding of the energy storage processes in 2D material-based EES devices is essential for optimizing their chemical composition, surface chemistry, morphology, and interlayer structure to enhance ion transport, promote redox reactions, suppress side reactions, and ultimately improve overall performance. This review provides a comprehensive overview of the characterization techniques employed to probe charge storage mechanisms in 2D and thin-layered material-based EES systems, covering optical spectroscopy, imaging techniques, X-ray and neutron-based methods, mechanical probing, and nuclear magnetic resonance spectroscopy. We specifically highlight the application of these techniques in elucidating ion transport dynamics, tracking redox processes, identifying degradation pathways, and detecting interphase formation. Furthermore, we discuss the limitations, challenges, and potential pitfalls associated with each method, as well as future directions for advancing characterization techniques to better understand and optimize 2D material-based electrodes.