Background: Calcium is essential for bone health, but its intake remains inadequate in populations with limited dairy consumption. Fish bones, abundant in calcium and phosphorus, represent a largely untapped natural resource for dietary calcium supplementation. The application of high-energy ball milling (HEM) presents a promising strategy to enhance calcium bioavailability by producing particles at the nanoscale. Methods: This study used HEM to convert fish bones from Euthynnus affinis (tuna) and Lutjanus sp. (snapper) into nanoparticles. The resulting powder was analyzed for particle size, morphology, crystallinity, thermal, flowability, hygroscopicity, mineral composition, and proximate constituents. Results: The HEM process successfully reduced the particle size of snapper and tuna bone powder to 729.83 and 847.93 nm, respectively, without altering their crystallinity. Morphological analysis revealed irregularly shaped particles, while thermal analysis indicated an exothermic decomposition pattern. No hygroscopic properties were observed in any of the samples. The nanonization process preserved the intrinsic mineral composition of the fish bones. Calcium/Phosphorus ratios remained >1.8. Elemental analysis confirmed high levels of calcium, phosphorus, and essential minerals such as potassium, magnesium, and sodium, while the protein and ash contents met nutritional standards. Conclusions Fish bone-derived nanoparticles produced via HEM exhibit advantageous physicochemical characteristics for nutraceutical applications and represent a promising source of bioavailable calcium to support bone health.