This work aims to evaluate the potential use of natural wastes (in particular, clam shells) to synthesize one of the most well-known and versatile materials from the phosphate mineral group, hydroxyapatite (HAP). The obtained material was characterized in terms of morphology and composition using several analytical methods (scanning electron microscopy—SEM, X-ray diffraction—XRD, X-ray fluorescence—XRF, Fourier transform infrared spectroscopy—FTIR, thermal analysis—TGA, and evaluation of the porosity and specific surface characteristics by the Brunauer–Emmett–Teller—BET method) in order to confirm the successful synthesis of the material and to evaluate the presence of potential secondary phases. The developed material was further doped with iron oxide (HAP-Fe) using a microwave-assisted method, and both materials were evaluated in terms of photocatalytic activity determined by the photodecomposition of methylene blue (MB) which served as a contaminant model. The best results (approx. 33% MB degradation efficiency, after 120 min. of exposure) were obtained for the hydroxyapatite material, superior to the HAP-Fe composite (approx. 27%). The utilization of hydroxyapatite obtained from clam shells underscores the importance of sustainable and eco-friendly practices in materials syntheses. By repurposing waste materials from the seafood industry, we not only reduce environmental impact, but also create a valuable resource with diverse applications, contributing to advancements in both healthcare and environmental protection.