Hydroxyapatite (HAp) Ca10(PO4)6(OH)2 is a compound that has stable chemical properties, composition, and an affinity for human bone. As a result, it can be used in odontology, cancer treatment, and orthopedic grafts to repair damaged bone. To produce calcined HAp at 600 °C with different pH values, a wet chemical precipitation method was employed. All synthesized HAp samples were characterized by X-ray diffraction (XRD), Raman spectroscopy, scanning electron microscopy (SEM), transmission electron microscopy (TEM), Fourier-transform infrared spectroscopy (FTIR), photoluminescence (PL), Zeta potential, and positron annihilation lifetime spectroscopy (PALS). The XRD results revealed that all calcined HAp samples were formed in a hexagonal structure with a preferred (002) orientation at different pH values. The crystal size of the samples was determined using the Scherrer equation, which ranged from 16 to 25 nm. The SEM and TEM results showed that the morphology of the samples varied from nanorods to nanospheres and rice-like structures depending on the pH value of the sample. The PL measurements indicated that the blue and green emission peaks of HAp were due to defects (bulk, surface, and interface) in the samples, which created additional energy levels within the band gap. According to Zeta potential measurements, the charge carrier changed from a positive to negative value, ranging from 3.94 mV to − 2.95 mV. PALS was used to understand the relationship between the defects and the photoluminescence (PL) properties of HAp. Our results suggest that HAp nanoparticles have excellent potential for developing non-toxic biomedical and optical devices for phototherapy.