Nanostructuring is a promising approach for enhancing thermoelectric properties of existing abundant and compatible materials such as silicon and silicon-based compounds. Recent works on different nanostructures have presented silicon-based materials as outstanding candidates for their implementation in thermoelectric generators. The compatibility of silicon with mainstream technologies, such as microelectronics and micro- and nano-fabrication, has attracted attention due to the integration of some of its nanostructures in micro-thermoelectric generators for energy harvesting applications. This topical review is focused on the most recent advances in fabrication, characterization and device integration of silicon-based thermoelectric nanomaterials, offering an outlook with an application-oriented focus. In particular, the use of doped silicon, silicon–germanium and silicides in the form of nanowires, thin films and superlattices as well as porous, nano-crystalline and nano-composite bulk is covered. Moreover, this paper provides future perspectives and research directions on the integration of silicon-based materials for energy applications in light of the recent findings reviewed.