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Abstract Non‐equilibrium defects often dictate the macroscopic properties of materials. They largely define the reversibility and kinetics of processes in intercalation hosts in rechargeable batteries. Recently, imaging methods have demonstrated that transient dislocations briefly appear in intercalation hosts during ion diffusion. Despite new discoveries, the understanding of impact, formation and self‐healing mechanisms of transient defects, including and beyond dislocations, is lacking. Here, operando X‐ray Bragg Coherent Diffractive Imaging (BCDI) and diffraction peak analysis capture the stages of formation of a unique metastable domain boundary, defect self‐healing, and resolve the local impact of defects on ionic diffusion in Na_xNi_1−yMn_yO₂intercalation hosts in a charging sodium‐ion battery. Results, applicable to a wide range of layered intercalation materials due to the shared nature of framework layers, elucidate new dynamics of transient defects and their connection to macroscopic properties, and suggest how to control the nanostructure dynamics.