The effect of low-energy ion irradiation on the nanolaminated Ti3AlC2 is investigated by means of X-ray diffraction, transmission electron microscopy, electron energy loss and X-ray absorption spectroscopy. The chemical sensitivity and local order probing from core-loss edges provide new insights into the structural modifications induced under irradiation. From the analysis of the C K energy loss near-edge structure and Al K X-ray absorption near-edge structure by ab initio calculations, the influence of the layered structure of this compound on the irradiation damage is demonstrated, and damage is found to be preferentially localized in the aluminum planes of the structure. On the basis of comparisons between calculations and experimental spectra, a structural model is proposed for the irradiated state. This study emphasizes the utility of core-loss fine structure analysis to enhance understanding of ion irradiation-induced damage in complex crystalline materials.