Chemical functionalization of semiconductor surfaces, particularly silicon oxide, has enabled many technologically important applications (e.g., sensing, photovoltaics, and catalysis). For such processes, hydroxyl groups terminating the oxide surface constitute the primary reaction sites. However, their reactivity is often poor, hindering technologically important processes, such as surface phosphonation requiring a lengthy postprocessing annealing step at 140 °C with poor control of the bonding geometry. Using a novel oxide-free surface featuring a well-defined nanopatterned OH coverage, we demonstrate that hydroxyl groups on oxide-free silicon are more reactive than on silicon oxide. On this model surface, we show that a perfectly ordered layer of monodentate phosphonic acid molecules is chemically grafted at room temperature, and explain why it remains completely stable in aqueous environments, in contrast to phosphonates grafted on silicon oxides. This fundamental understanding of chemical activity and surface stability suggests new directions to functionalize silicon for sensors, photovoltaic devices, and nanoelectronics.