Thanks to its high temperature properties and relatively good behaviour under irradiation, the MgAl 2O 4 spinel is considered as a possible material to be used as inert matrix for the minor actinides burning. However, it is known to damage at high fluences. Several studies have shown that the damages induced by irradiation lead first to structural modifications and second to an amorphisation inducing an important swelling. In order to propose a better description of these structural modifications, we have irradiated different spinels at room temperature at Grand Accélérateur National d’Ions Lourds at Caen (GANIL) facility with swift Kr ions. The irradiation damages were characterised by Raman analysis and X-ray diffraction. Three different materials were irradiated, MgAl 2O 4 and the isomorphic spinels ZnAl 2O 4 and MgCr 2O 4, this allowing a better X-ray analysis of the cations distributions. Comparing our results with previously published ones, we show that the apparent damage of these materials do not depend on the irradiation conditions. In addition, we have unambiguously observed that the first damage stage is not a phase transformation but an order–disorder transition of the cationic sub-lattice. On the other hand, for the three materials, the cations are distributed on the classical 8a and 16d sites. The inversion rates we derive are however much higher than in non-irradiated materials at high temperatures. But in the Mg-materials, the cations are also located on the normally empty sites 16c and 48f, leading to highly disordered structures. We have then performed isochronal annealings, which show that the disorder recovers in one stage (ZnAl 2O 4) or in two different stages (MgAl 2O 4 and MgCr 2O 4). The second stage can be attributed to the healing of the cation inversion rate, the first one to the displacement of the cations from the forbidden to the normal positions. In the three cases, the initial structure is totally healed after annealing at 1000 °C. These results could give some clues to explain the amorphisation stage of the spinels under irradiation and help in selecting a better inert matrix material.