Chemical or physical manipulation of a specific type of microorganisms from a mixed population poses a great challenge. Current techniques mostly include laborious and time-consuming hands-on work under the microscope or expensive sophisticated flow cytometric and cell sorting technologies. We propose the use of multifunctional magnetic Halloysite nanotubes (HNTs), which could specifically bind to their target microorganism and also deliver bioactive compounds or moieties. HNTs are naturally-occurring clay nanoparticles with a hollow tubular shape. The different chemical composition of the nanotube external and inner surfaces (silica and alumina, respectively) allows for various approaches for their orthogonal chemical modifications. Such modifications could include conjugation of a recognition element for a specific type of microorganism on the HNTs external surface and their magnetization to enable a straightforward particle manipulation. The latter 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. While, targeting specific bacteria is successfully realized by conjugation of specific antibodies to HNTs outer surface. We show that the resulting multifunctional HNTs with their high specific surface area and unique tubular structure allow us to easily manipulate bacteria, while making them ideal for future loading and controlled release of various cargos.