On the basis of Pauling's first rule for ionic bonding, the coordination number of cations with oxygen anions can be determined by comparison of their relative ionic size ratio. In contrast to simple oxides, various site occupancies by multicomponent cations with similar sizes usually occur in complex oxides, resulting in distinct physical properties. Through an unprecedented combination of in situ high-temperature high-resolution electron microscopy, crystallographic image processing, geometric phase analysis, and neutron powder diffraction, we directly demonstrate that while the initial crystallites after nucleation during crystallization have a very high degree of ordering, significant local cation disordering is induced by rapid crystal growth in Li-intercalation metal-phosphate nanocrystals. The findings in this study show that control of subsequent crystal growth during coarsening is of great importance to attain a high degree of cation ordering, emphasizing the significance of atomic-level visualization in real time.