Recent breakthroughs in nanotechnology have made various nanostructured materials more affordable for a broader range of applications. Although we are still at the beginning of exploring the use of these materials for biocatalysis, various nanostructures have been examined as hosts for enzyme immobilization via approaches including enzyme adsorption, covalent attachment, enzyme encapsulation, and sophisticated combinations of methods. This review discusses the stabilization mechanisms behind these diverse approaches; such as confinement, pore size and volume, charge interaction, hydrophobic interaction, and multipoint attachment. In particular, we will review recently reported approaches to improve the enzyme stability in various nanostructures such as nanoparticles, nanofibers, mesoporous materials, and single enzyme nanoparticles (SENs). In the form of SENs, each enzyme molecule is surrounded with a nanometer scale network, resulting in stabilization of enzyme activity without any serious limitation for the substrate transfer from solution to the active site. SENs can be further immobilized into mesoporous silica with a large surface area, providing a hierarchical approach for stable, immobilized enzyme systems for various applications, such as bioconversion, bioremediation, and biosensors.