Solid-solid phase transitions are processes ripe for the discovery of correlated atomic motion in crystals. Here, we monitor an order-disorder transition in real-time in nanoparticles of the super-ionic solid, Cu2-xSe. The use of in-situ high-resolution transmission electron microscopy allows the spatiotemporal evolution of the phase transition within a single nanoparticle to be monitored at the atomic level. The high spatial resolution reveals that cation disorder is nucleated at low co-ordination, high energy sites of the nanoparticle where cationic vacancy layers intersect with surface facets. Time-dependent evolution of the reciprocal lattice of individual nanoparticles shows that the initiation of cation disorder is accompanied by a ~3% compression of the anionic lattice, establishing a correlation between these two structural features of the lattice. The spatiotemporal insights gained here advance understanding of order-disorder transitions, ionic structure and transport, and the role of nanoparticle surfaces in phase transitions.