Inorganic hydroxyapatite nanoparticles (HANPs) and two kinds of organic biomolecules (i.e., fluorescent dye rhodamine 6G and protein lysozyme) were coencapsulated into alginate microspheres through an air dynamical atomization with optimized operation conditions. The synthesized microspheres have several advantages: HANP provides osteoconductivity and mechanical strength, rhodamine 6G (R6G) and lysozyme act as model drugs, and alginate provides excellent biocompatibility and carboxylate functionality. The results of fluorescent microscopic images indicated the successful dual encapsulation of HANPs and lysozyme inside the alginate microspheres. Furthermore, the results of 3- (4,5-cimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide assay showed that the fabricated alginate microspheres could be uptaken by HepG2 without apparent cytotoxicity. The dual encapsulated alginate microspheres fabricated in this study show great potential in many biomedical applications.