This work reports on the influence of 5 MeV electron beam radiations on the morphological features and chemical structure of magnesium-doped hydroxyapatite/chitosan composite coatings generated by the magnetron sputtering technique. The exposure to ionizing radiation in a linear electron accelerator dedicated to medical use has been performed in a controllable manner by delivering up to 50 Gy radiation dose in fractions of 2 Gy radiation dose per 40 s. After the irradiation with electron beams, the surface of layers became nano-size structured. The partial detachment of irradiated layers from the substrates has been revealed only after visualizing their cross sections by scanning electron microscopy. The energy dispersive X-ray spectral analysis of layer cross-sections indicated that the distribution of chemical elements in the samples depends on the radiation dose. The X-ray photoelectron spectroscopy, Fourier transform infrared spectroscopy and X-ray diffraction analysis have shown that the physicochemical processes induced by the ionizing radiation in the magnesium doped hydroxyapatite/chitosan composite coatings do not alter the apatite structure, and Mg remains bonded with the phosphate groups.