The assembly of multifunctional nanocomposite materials is demonstrated by exploiting the molecular sieving property of SBA-16 nanoporous silica and using it as a template material. The cages of the pore networks are used to host iron oxide magnetic nanoparticles, leaving a pore volume of 0.29 cm3 g−1 accessible for drug storage. This iron oxide–silica nanocomposite is then functionalized with amine groups. Finally the outside of the particle is decorated with antibodies. Since the size of many protein molecules, including that of antibodies, is too large to enter the pore system of SBA-16, the amine groups inside the pores are preserved for drug binding. This is proven using a fluorescent protein, fluorescein-isothiocyanate-labeled bovine serum albumin (FITC-BSA), with the unreacted amine groups inside the pores dyed with rhodamine B isothiocyanate (RITC). The resulting nanocomposite material offers a dual-targeting drug delivery mechanism, i.e., magnetic and antibody-targeting, while the functionalization approach is extendable to other applications, e.g., fluorescence–magnetic dual-imaging diagnosis.