This paper reports modifications of the chemical and structural properties of MgAl 2 O 4 single crystals implanted with Cs ions and submitted to high-temperature annealing. The composition changes, the damage created in the three sublattices (Al, Mg and O) of the crystals, and the behavior of implanted ions were studied by Rutherford backscattering and channeling experiments as a function of the Cs fluence and annealing temperature. The data show that annealing above 700–800 °C induces a huge modification of the stoichiometry of the material, a decrease of the lattice disorder, and an increase of the fraction of Cs atoms located in substitutional lattice sites. These results have to be taken into account for the future use of spinel as a matrix for the transmutation of nuclear waste.