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Abstract Single-photon emitters are crucial building blocks for optical quantum technologies. Hexagonal boron nitride (hBN) is a promising two-dimensional material that hosts bright, room-temperature single-photon emitters. However, photo instability is a persistent challenge preventing practical applications of these properties. Here, we reveal the ubiquitous photobleaching of hBN vacancy emitters. Independent of the source or the number of hBN layers, we find that the photobleaching of a common emission at 1.98 ± 0.05 eV can be described by two consistent time constants, namely a first bleaching lifetime of 5 to 10 s, and a second bleaching lifetime in the range of 150 to 220 s. Only the former is environmentally sensitive and can be significantly mitigated by shielding O₂, whereas the latter could be the result of carbon-assisted defect migration. Annular dark-field scanning transmission electron microscopy of photobleached hBN allows for visualizing vacancy defects and carbon substitution at single atom resolution, supporting the migration mechanism along with X-ray photoelectron spectroscopy. Thermal annealing at 850 °C of liquid exfoliated hBN eliminates both bleaching processes, leading to persistent photostability. These results represent a significant advance to potentially engineer hBN vacancy emitters with the photostability requisite for quantum applications.