Successful direct route production of silicon nanostructures from diatomaceous earth (DE) on a single crystalline silicon wafer via the magnesiothermic reduction reaction is reported. The formed porous coating of 6 µm overall thickness contains silicon as the majority phase along with minor traces of Mg, as evident from SEM-EDS and the Focused Ion Beam (FIB) analysis. Raman peaks of silicon at 519 cm and 925 cm were found in both the film and wafer substrate, and significant intensity variation was observed, consistent with the SEM observation of the directly formed silicon nanoflake layer. Microstructural analysis of the flakes reveals the presence of pores and cavities partially retained from the precursor diatomite powder. A considerable reduction in surface reflectivity was observed for the silicon nanoflakes, from 45% for silicon wafer to below 15%. The results open possibilities for producing nanostructured silicon with a vast range of functionalities.