Molecular design and development of protein assemblies with functional molecules has recently been intriguing subject in bionanotechnology and biomaterials because protein assemblies can provide unique chemical environments which can immobilize functional substances such as metal ions, metal complexes, nanomaterials, and proteins. In this article, we focus on our recent progress of protein assemblies of cages and crystals as molecular templates for reaction vessels and molecular delivery. First, ferritin engineering for tandem reactions by two different organometallic complexes in the cage and delivery of gaseous molecules using the cage into the cells is reported. Second, protein crystals are developed in the applications as solid catalysis and extracellular matrix by immobilization of metal complexes in the solvent channels of protein crystals. Finally, in vivo protein crystal engineering toward the creation of bio-hybrid solid materials in living cells is described.