<p>A series of porous hydroxyapatite (HAp) nanoparticles were synthesized through a novel route using silica nanoparticles of different sizes as nucleating agents and sodium alendronate as a growth-controlling molecule. A comprehensive characterization of the structural and morphological properties of the materials was carried out to assess the influence of the nucleating agent size on the resulting HAp nanoparticles. The samples—HAp-Si65, HAp-Si103, and HAp-Si355—were derived from SiO₂ nanoparticles with hydrodynamic diameters of (65 ± 20) nm, (103 ± 35) nm, and (355 ± 94) nm, respectively. X-ray diffraction (XRD), transmission electron microscopy (TEM), attenuated total reflectance infrared spectroscopy (ATR-FTIR), and thermogravimetric analysis (TGA) revealed only minor differences in crystallinity, shape, surface functional groups, and thermal behaviour among the samples. However, both the surface area and total pore volume increased with larger SiO₂ particle sizes. Notably, HAp-Si65 exhibited significant micropore volume. To evaluate how pore size distribution affects the adsorption performance, kinetic and equilibrium adsorption experiments were conducted using methylene blue (MB), a widely used cationic dye and model pollutant in wastewater treatment studies. In addition, MB acts as a photosensitizer, making it particularly relevant for studies involving photocatalytic degradation and light-assisted remediation processes. The results demonstrate that the micro-mesoporous characteristics of the HAp nanoparticles play a critical role in MB adsorption capacity, along with other contributing factors. The findings provide insights into the relationship between synthesis parameters, structural features, and adsorptive performance, offering guidance for the design of efficient and heavy-metal-free HAp-based adsorbents for environmental applications.</p>