The holo-allophycocyanin-α subunit, which has various reported pharmacological uses, was biosynthesized with both Strep-II-tag and His-tag at the N-terminal in Escherichia coli. The streptavidin-binding ability resulting from the Strep II-tag was confirmed by Western blot. Additionally, the metal-chelating ability deriving from the His-tag not only facilitated its purification by immobilized metal-ion affinity chromatography but also promoted its immobilization on Zn (II)-decorated silica-coated magnetic nanoparticles. The holo-allophycocyanin-α subunit with streptavidin-binding ability was thereby immobilized on magnetic nanoparticles. Magnetic nanoparticles are promising as drug delivery vehicles for targeting and locating at tumors. Thus, based on genetic engineering and nanotechnology, we provide a potential strategy to facilitate the biomodification and targeted delivery of pharmacological proteins.