Synchrotron X-ray microtomography was used to observe the shrinkage and annihilation behaviors of hydrogen micropores in three dimensions during hot and cold plastic deformation of an Al–Mg alloy. Whether complete healing of micropores is achieved after plastic deformation was examined by exposing the material to a high temperature after plastic deformation. Although micropores generally show a pattern of shrinking and closing, closer inspection of a single specimen revealed a variety of geometrically variable behaviors. It is noteworthy that some of the micropores are reinitiated in positions identical to those before their annihilation, even after an 8–22% macroscopic strain has been further applied after annihilation. We attribute local variations such as these to significant local strain variation, which we measured in a series of tomographic volumes by tracking the microstructural features.