Only with appropriate coatings and coating techniques the use of nanoparticles is possible for biomedical applications. The appropriate choice of the coating material and techniques helps to render the particles biocompatible, colloidally and chemically stable, and biological functional. Most often a single surface coating is not sufficient for application of the particles and subsequent coupling to a biological compound needs to be done. Therefore the coating needs to allow as well for further surface functionalization as the binding of proteins, medical drugs or other biomolecules to the system and to fine-tune the surface to the desired application. This thesis work focused on coating and encapsulation of superparamagnetic iron oxide (SPION) and fluorescent ZnS:Mn2+ with inorganic (silica, calcium phosphate) and organic material (protein, polyethylenimine). In the foreground of the developed coatings were applications in biotechnology and medicine, but also the effects of the coating on the physical properties of nanoparticles were examined. Different coating methods by utilizing inorganic (silica) and organic substances (polyethylenimine) were developed for the production of superparamagnetic iron oxide nanoparticle-containing beads for mRNA extraction, magnetic separation, or transfection, which will be discussed in this work. Only by combination of a multitude of single SPION in a bead a strong response to a magnet with respect to the sedimentation velocity can be achieved. As well, different species of nanoparticles with different surfaces and properties, the SPIONs and fluorescent ZnS:Mn2+, were combined in a single bead by a microemulsion encapsulation method. Especially sol-gel coating techniques showed a high versatility in encapsulation and bead formation, regarding the control of magnetic loading, particle size, and surface charge.