Thermoelectric converters based on silicon nanostructures offer exciting opportunities for higher efficiency, lower cost, ease of manufacturing, and integration into circuits. This paper considers phonon transport in a broad range of nanostructured materials made from Si, Ge, and their alloys. Our model based on the phonon Boltzmann transport equation captures the lattice thermal transport in silicon–germanium (SiGe) nanostructures, including thin films, superlattices (SLs), and nanocomposites. In nanocomposites, the model captures the grain structure using a Voronoi tessellation to mimic the grains and their size distribution. Our results show thermal conductivity in SiGe nanostructures below their bulk counterparts and reaching almost to the amorphous limit of thermal conductivity. We also demonstrate that thermal transport in SiGe nanostructures is tuneable by sample size (thin films), period thickness (SLs), and grain size (nanocomposites) through boundary scattering. Our results are relevant to the design of nanostructured SiGe alloys for thermoelectric applications.