To assess the application potential of novel biomaterials, their behaviour in model media and upon sterilization should be investigated, as well as the stability related to their storage conditions. Such data are lacking for Mg-substituted HAP (Mg-HAP). Therefore, the changes in the local structure of non-substituted and Mg-HAP after irradiation and immersion in corrected simulated fluid and saline solution for 28 days were followed by electron paramagnetic resonance (EPR) spectroscopy for the first time. To better understand the stability of radical species induced by sterilization, EPR spectra of samples kept for 2 h at temperatures up to 373 K were recorded to provide an insight into the stability of the sample storage conditions by the accelerated aging method. Samples were characterized by PXRD, FTIR, SEM, EDS, AAS and TGA. Results confirmed that irradiation does not induce changes in the composition or the structure of any of the investigated materials. Fading or the complete disappearance of radical signals in the EPR spectra after immersion in both media was accompanied by the disappearance of other phases formed as a minor byproduct in the synthesis of substituted HAP, as confirmed by PXRD and FTIR analysis. Obtained results confirm the great potential of Mg-HAPs for biomedical applications, although closer attention should be given to the processes related to sample storage stability at different temperatures.