Protein-coated magnetic nanoparticles are promising candidates for various medical applications. Prior to their application into a biological system, one has to guarantee that the particle dispersions are free from pathogens or any other microbiologic contamination. Furthermore, to find entrance into clinical routine, the nanoparticle dispersions have to be storable for several months. In this study, we tested several procedures for sterilization and preservation of nanoparticle containing liquids on their influence on the integrity of the protein coating on the surface of these particles. For this, samples were treated by freezing, autoclaving, lyophilization, and ultraviolet (UV) irradiation, and characterized by means of dynamic light scattering, determination of surface potential, and gel electrophoresis afterwards. We found that the UV sterilization followed by lyophilization under the addition of polyethylene glycol are the most promising procedures for the preparation of sterilized long-term durable protein-coated magnetic nanoparticles. Ongoing work is focused on the optimization of used protocols for UV sterilization and lyophilization for further improvement of the storage time.