Selenium (Se) is an essential micronutrient, recognized for its role in cellular redox systems and its therapeutic potential in cancer treatment. Organic selenium compounds, particularly selenocystine (SeCys), have demonstrated anticancer efficacy due to the ability to induce apoptosis and enhance the effects of chemotherapy agents. Recent studies have shown that SeCys exhibits selective toxicity against cancer cells while sparing normal cells. Unfortunately, its clinical application is limited by stability and solubility concerns. A possible solution to overcome these hurdles comes from recent advances in functionalized nanomaterials. In this study, we investigate the possible incorporation of SeCys with hydroxyapatite nanoparticles (HASeCys) via various methods (adsorption, co-precipitation, and co-precipitation through thermal decomplexation), resulting in the formation of nanocomposites with elemental selenium. The highest elemental selenium yield was achieved with a thermal decomplexing co-precipitation, highlighting the influence of synthesis parameters on Se allotrope formation. Finally, as a preliminary investigation, the HASeCys samples were tested on a panel of cancer cell lines, showing an interesting activity when the hydroxyapatite nanocrystals were functionalized with both crystalline gray and amorphous red selenium.