Ion-beam-induced microstructures in magnesium aluminate (MgAl₂O₄) spinel have been examined using transmission electron microscopy (TEM). Irradiations were performed at cryogenic temperature (~120 K) on MgAl₂O₄ spinel single-crystal surfaces with (111) orientation, using 180 keV neon (Ne⁺) ions to ion fluences ranging from 10¹⁶ to 10¹⁷ Ne⁺ cm^-2. Cross-sectional TEM observations indicated that the MgAl₂O₄ spinel transforms first into a metastable crystalline phase and then into an amorphous phase under these irradiation conditions. On the basis of selected-area electron diffraction and high-resolution TEM, we concluded that Ne-ion-beam irradiation induces an ordered spinel-to-disordered rock-salt-like structural phase transformation. Atomistic structures of amorphous MgAl₂O₄ were also examined on the basis of atomic pair distribution functions. We compared the experimentally obtained results with previous theoretically calculated results for the metastable and amorphous phases of MgAl₂O₄, and discussed the validity of the proposed ion-beam-induced structural changes in MgAl₂O₄ spinel.