Halloysite nanotubes (HNTs) are naturally-occurring tubular clay particles which hold fascinating opportunities as an emerging affordable solution for biomedical challenges. HNTs large pore volume and high specific surface area, in combination with their biocompatibility make them ideal as nano-carriers for bioactive compounds. We design and synthesize multifunctional magnetic HNTS (m-HNTs), which could specifically bind to target bacterial cells and manipulate them, as well as deliver a bioactive cargo. HNTs magnetization is achieved by co-precipitation of iron(II) and iron(III) cations onto the negatively-charged HNTs, followed by the oxidation of the iron into magnetite. Next, the HNTs are functionalized by specific antibodies for targeting model bacterial cells. The hydroxyls onto the HNTs surface are activated by silanization and carboxylation for superior suspendability in aqueous conditions. The resulting carboxyl groups are conjugated with protein A to which the antibody binds in a proper orientation. We show the successful decoration of HNTs surface with magnetic nanoparticles in a one-pot simultaneous magnetization and silanization reaction. In addition, the resulting multifunctional HNTs with their high specific surface area and unique tubular structure exhibits affinity to a model microorganism (E. coli), making them ideal for future loading and targeted release of various cargos.