In this research, HAp nanocrystals were synthesized using conventional wet chemical precipitation methods using various organic modifiers, including urea, palmitic acid, and naphthalene. Ethanol and isopropyl alcohol (IPA) were used as solvents in this process. Different characterization techniques, namely X-ray diffraction (XRD), scanning electron microscopy (SEM), and UV-vis absorption spectroscopy, were employed to ascertain the formation of HAp nanocrystals. Numerous structural parameters, including lattice parameters, unit cell size, volume of the unit cell, specific surface area, degree of crystallinity, dislocation density, macrostrain, and crystallinity index, were assessed using XRD data. The linear straight-line method of Scherrer's equation, Monshi–Scherrer's method, the Williamson–Hall method, the size–strain plot method, the Halder–Wagner method, and Sahadat–Scherrer's model were applied to compute the crystallite size of the synthesized HAp samples. All the synthesized HAp has crystalline structures within the permissible range of 1–150 nm which were estimated from the XRD data using the mentioned models. However, the values for strain (from −3 × 10⁻⁴ to 6.4 × 10⁻³), strain (from −9.599 × 10⁴ to 7 × 10¹⁰ N m⁻²), and energy density (from −11 × 10¹¹ to 2 × 10⁷ J m⁻³) were also calculated for the synthesized samples. In addition, the optical band gap energy of the synthesized HAp was computed (5.89 to 6.19 eV). The synthesis media have a control on the crystallographic planes, e.g. in the case of the ethanol medium, the (110) plane exhibited significant intensity (which could potentially serve as a driving force for enhancing photocatalytic activity). The use of 100% ethanol HAp yields the most favorable outcome regarding both the degradation percentage (91.79%) and degradation capacity (7%) for the Congo red dye.