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In this study, we evaluated the catalytic properties of hydroxyapatite (HA) nanoparticles (NPs) doped with Fe3O4/γ-Fe2O3 for the degradation of methylene blue (MB) dye using a photo-Fenton process at pH 2.5, 7.0, and 9.0. The HA NPs were characterized using X-ray diffraction, scanning electron microscopy, Fourier-transform infrared spectrometry, Raman spectroscopy, thermogravimetric analysis, fluorescence spectrometry, and point of zero charge experiments. Upon using unmodified HA NPs, 1.33 mL of H2O2 30% (v/v), and ultraviolet radiation (125 W Hg lamp), the discoloration values achieved at pH 2.5, 7.0, and 9.0 were 88.4, 44.8, and 58.1%, respectively. For the HA NPs modified with Fe3O4/γ-Fe2O3, the composition Ca2.5FeII2.5FeIII5(PO4)6(OH)2 yielded the best results during the photo-Fenton-based process, and discolorations of 100, 100, and 95.2% were achieved at pH 2.5, 7.0, and 9.0, respectively. To confirm the effectiveness of the Ca2.5FeII2.5FeIII5(PO4)6(OH)2 NPs, the total organic carbon (TOC) and toxicity effects on Lactuca sativa L. were evaluated, and reproducibility tests were performed. The TOC removal of the Ca2.5FeII2.5FeIII5(PO4)6(OH)2 NPs was ca. 90% and the toxicity of the MB dye was eliminated after 120 min of reaction; moreover, the NPs retained their physical stability and activity and were reused for 11 consecutive degradation experiments.