Developing efficient energy storage systems remains one of the biggest challenges in the transition towards a sustainable energy landscape. Many energy-storage processes rely on phase transformations of nanomaterials in reactive environments. Compared to their bulk counterparts, nanostructured materials exhibit fast charging and discharging kinetics, resistance to defects formation, and thermodynamics that can be modulated by size effects. However, in ensemble studies of these materials, it is often difficult to discriminate between intrinsic size-dependent properties and effects due to sample size and shape dispersity. Here, we use a wide range of in-situ transmission electron microscopy techniques to reconstruct the absorption of hydrogen in individual palladium nanocrystals. Using electron energy-loss spectroscopy, dark-field imaging and electron diffraction, we shed light on the role of surface energy, crystallographic defects, lattice strain, and particle aspect ratio on the thermodynamics and kinetics of phase transformation in these nanostructured systems [1-4]. Our results provide a general framework for studying phase transitions in individual nanocrystals and highlight the importance of single-particle approaches to the characterization of functional nanomaterials.