With the advent of recombinant technology, a wide variety of biocompatible therapeutic proteins can be produced with relative ease. These proteins are formulated and subsequently administered in patients to treat various of diseases in a more effective and targeted manner. At the level of formulation development, protein molecules can be physically and/or chemically-conjugated to a wide array of naturally-occurring, semi-synthetic and synthetic biomaterials to form different types of protein delivery systems. Depending on their architecture and the extent of protein-scaffold interactions, these delivery systems can modify the pharmacokinetic and pharmacodynamic properties of the proteins. The versatility of polymer-based protein delivery systems such as micro/nanoparticles, hydrogels, porous scaffolds and fibrous scaffolds means it is possible to alter the spatial distribution of the protein load within the system as well as the protein release kinetics.These can then influence the ability of the protein molecules to exert their effects in their immediate microenvironments, be it to kill cancer cells or to recruit stem/progenitor cells. In this Chapter we discuss the production of protein therapeutics and the application of polymer-based biodegradable delivery systems for these proteins which include nanoparticles and scaffolds. We also include discussion of 'green synthesis' methods for production of these delivery systems.