Application-oriented research on protein-based nanocages such as ferritins, encapsulins, viral cage structures, carboxysomes, and others has become increasingly important in recent years and has potential applications in biotechnology, biochemistry, and medicine. The focus of this chapter is on the applications of this self-assembling protein cages in (bio)organic catalysis. The discussion covers two main areas: enzyme-based and organometallic systems. Various studies are discussed that explore the encapsulation of enzymes with metal ions or metal clusters as cofactors as well as research describing encapsulation of organometallic catalysts in protein compartments.