Combining experimental design with advanced characterisation methods provides a valuable opportunity to deepen our understanding of catalytic processes and their underlying mechanisms. Here, a series of hydroxyapatite doped with Fe2+ at different molar loadings noted HAP-FeX% (X = 1; 5.5 and 10; Ca/Fe molar ratio) were elaborated using a one-pot synthesis method. Characterization of these catalysts by various techniques such as ICP, BET/BJH, TGA/DSC, XRD, Raman, UV–visible, TPD-NH3, SEM, and TEM revealed substantial Fe2+ oxidation during synthesis, inducing changes in the morphological and physical-chemical characteristics of HAP caused by Fe3+/Ca2+ substitution. Furthermore, the synthesis produced nanoparticles (approximately 0.30 nm in size) on the hydroxyapatite surface, resulting from the precipitation of Fe/O phases. The catalysts exhibited good catalytic performance in methylene blue (MB) degradation through the photo-Fenton process (95 %). The Ca/Fe molar ratio = 8.8 %, [H2O2] = 2.8 mmol L−1, and pH = 8.8 were optimized using the design of experiments (DOE) via response surface methodology (RSM). A mathematical model was developed to determine the influence of the Ca2+/Fe3+ substitution and the Fe/O phase on the catalytic activity. The results revealed the role of the Fe/O phase in the reaction initiation and the surface modification induced by Ca2+/Fe3+ substitution to facilitate the reaction chain.