The electrical quality of functionalized, oxide-free silicon surfaces is critical for chemical sensing, photovoltaics, and molecular electronics applications. In contrast to Si/SiO2 interfaces, the density of interface states (Dit) cannot be reduced by high temperature annealing because organic layers decompose above 300 °C. While a reasonable Dit is achieved on functionalized atomically flat Si(111) surfaces, it has been challenging to develop successful chemical treatments for the technologically relevant Si(100) surfaces. We demonstrate here that recent advances in the chemical preparation of quasi-atomically-flat, H-terminated Si(100) surfaces lead to a marked suppression of electronic states of functionalized surfaces. Using a non-invasive conductance-voltage method to study functionalized Si(100) surfaces with varying roughness, a Dit as low as 2.5 × 1011 cm−2eV−1 is obtained for the quasi-atomically-flat surfaces, in contrast to >7 × 1011 cm−2eV−1 on atomically rough Si(100) surfaces. The interfacial quality of the organic/quasi-atomically-flat Si(100) interface is very close to that obtained on organic/atomically flat Si(111) surfaces, opening the door to applications previously thought to be restricted to Si(111).