Germanium is a critically important material for future complementary metal-oxide-semiconductor devices, however, to maximise its potential it is necessary to develop a robust passivation process that prevents Ge re-oxidation for a queue time of 24 h. Self-assembled monolayers (SAMs) of alkanethiols on Ge have previously been shown to inhibit oxidation; however, re-oxidation eventually occurs when exposed to ambient conditions. Herein, it is shown that humidity plays a key role in the degradation of the SAM, ultimately resulting in re-oxidation. To demonstrate this, thiol-passivated Ge(100) surfaces are exposed to controlled humidity environments with different levels of relative humidity (RH). The rate of re-oxidation of the Ge surfaces are tracked using X-ray photoelectron spectroscopy and water contact angle analysis to discern what role RH plays in the re-oxidation of the Ge and the degradation of the SAM passivation. Atomic force microscopy data is presented to show that humidity-mediated re-oxidation of the Ge has little or no impact on the route mean square roughness of those surfaces. Finally, atomistic modelling of thiol-SAM passivated Ge in the presence of water molecules has been studied using first principles density functional theory in order to simulate experimental conditions and to understand the atomic level processes that determine stability in hydrophilic and hydrophobic configurations.