The present review focuses on the proteins and peptides at the interfaces of nanostructured metals and semiconductors as a result of their use in synthesis in-situ and functionalization of nanostructures. We start the review with an introduction about the peculiar properties of nanostructured materials and their applications. In the following, the chemical and structural properties of peptides and proteins that allow their use as reducing, stabilizing, and functionalization agents are discussed. Proteins and peptides have not only the chemical groups for the metal ion reducing but also provide templates for directing the crystalline growing of nanostructures to the desired shapes and sizes. Proteins and peptides are also used mainly for the stabilization and functionalization of a diversity of nanostructured materials providing properties such as biocompatibility, plasmon-enhanced catalysis, sensing, micro/nanomotors, spin filters, and others. Nanostructured materials of metal oxides have mainly been functionalized with proteins and peptides to gain specific properties such as light harvesting and spin filters. Herein, we described the synthesis and functionalization of some types of nanostructured materials by using peptides and proteins. In the last part of the review, it is discussed the perspectives and challenges for the use of proteins and peptides in Nanotechnology.