Efficient delivery of nanosized drug formulations to the desired body sites is not always reached despite the rapid development of pharmaceutical nanotechnologies. In spite of the undoubted effect of the size for increased bioavailability and controlled drug delivery, submicrometer formulations also require a deeper level of design. The surface properties of the particles determine the stability of the particles, interactions with the body, and targeting potentials of drugs. Thus, the efficacy of the drug can be increased utilizing the surface layer of the nanoparticles. Influencing the surface characters of the drug is the main focus of the present work, which introduces a method for preparing nanoparticles with functional sites from low-solubility drugs using hydrophobin (HFB) proteins. Particles were prepared by precipitating a lipophilic drug (beclomethasone dipropionate) in water in the presence of the HFB proteins. Particle size below 200 nm could easily be reached with increasing HFB concentration. The particles were shown to be stable for at least 5 h in suspension, and they could be stored for longer periods of time after freeze-drying. Labeling studies using green fluorescent protein (GFP) genetically fused to a HFB clearly demonstrated that the surface of the nanoparticles was covered with the hydrophobins and that the surface could be further modified by utilizing fusion proteins. This provides a template for a variety of different functional surface-bound groups that could be tailored by modifying the hydrophilic side of the HFB via protein bioengineering. In this study, the combination of proteins and traditional pharmaceutical technology was used to synthesize functionalized protein-coated nanoparticles for drug delivery purposes.