Nanostructured materials are essential building blocks for the fabrication of new devices for energy harvesting/storage, sensing, catalysis, magnetic, and optoelectronic applications. However, because of the increase of technological needs, it is essential to identify new functional materials and improve the properties of existing ones. The objective of this Viewpoint is to examine the state of the art of atomic-scale simulative and experimental protocols aimed to the design of novel functional nanostructured materials, and to present new perspectives in the relative fields. This is the result of the debates of Symposium I "Atomic-scale design protocols towards energy, electronic, catalysis, and sensing applications", which took place within the 2018 European Materials Research Society fall meeting.