Phase transitions in reactive environments are crucially important in energy and information storage, catalysis and sensors. Nanostructuring active particles can yield faster charging/discharging kinetics, increased lifespan and record catalytic activities. However, establishing the causal link between structure and function is challenging for nanoparticles, as ensemble measurements convolve intrinsic single-particle properties with sample diversity. Here we study the hydriding phase transformation in individual palladium nanocubes in situ using coherent X-ray diffractive imaging. The phase transformation dynamics, which involve the nucleation and propagation of a hydrogen-rich region, are dependent on absolute time (aging) and involve intermittent dynamics (avalanching). A hydrogen-rich surface layer dominates the crystal strain in the hydrogen-poor phase, while strain inversion occurs at the cube corners in the hydrogen-rich phase. A three-dimensional phase-field model is used to interpret the experimental results. Our experimental and theoretical approach provides a general framework for designing and optimizing phase transformations for single nanocrystals in reactive environments.