The high-energy electron beams in transmission electron microscopes (TEM) are known to cause structural changes and damage in some materials. In this paper, we describe unique and reproducible TEM-induced changes to the morphology of amorphous metal oxide (Fe, Co, and Ni) nanoparticles. The studied particles were synthesized via literature methods and fully characterized by X-ray powder diffraction and time-resolved, low-dose TEM. As a result of electron beam irradiation, we observe these particles to transform from initially solid spheres to core/void/shell structures and eventually to hollow nanoparticles. The rate of these transformations depends on the size and composition of the particles but is not unique to the Fe oxide we previously reported. These data suggest that structural analysis of nanoparticles by TEM must consider the impact of the high-energy electron beam and use low-dose imaging.