β-Ga₂O₃ is an emerging ultra-wide bandgap semiconductor, holding a tremendous potential for power-switching devices for next-generation high power electronics. The performance of such devices strongly relies on the precise control of electrical properties of β-Ga₂O₃, which can be achieved by implantation of dopant ions. However, a detailed understanding of the impact of ion implantation on the structure of β-Ga₂O₃ remains elusive. Here, using aberration-corrected scanning transmission electron microscopy, we investigate the nature of structural damage in ion-implanted β-Ga₂O₃ and its recovery upon heat treatment with the atomic-scale spatial resolution. We reveal that upon Sn ion implantation, Ga₂O₃ films undergo a phase transformation from the monoclinic β-phase to the defective cubic spinel [Formula: see text]-phase, which contains high-density antiphase boundaries. Using the planar defect models proposed for the [Formula: see text]-Al₂O₃, which has the same space group as β-Ga₂O₃, and atomic-resolution microscopy images, we identify that the observed antiphase boundaries are the {100}1/4 ⟨110⟩ type in cubic structure. We show that post-implantation annealing at 1100 °C under the N₂ atmosphere effectively recovers the β-phase; however, nano-sized voids retained within the β-phase structure and a [Formula: see text]-phase surface layer are identified as remanent damage. Our results offer an atomic-scale insight into the structural evolution of β-Ga₂O₃ under ion implantation and high-temperature annealing, which is key to the optimization of semiconductor processing conditions for relevant device design and the theoretical understanding of defect formation and phase stability.