Modification of hydroxyl-terminated self-assembled monolayer (HO-SAM) surfaces by collision of low-energy (15 eV) hyperthermal Si(CH3)3+ ions is shown to lead to Si-O bond formation and terminal trimethylsilyl ether formation. Modification was verified by in situ mass spectrometry using chemical sputtering with CF3+ ions (70 eV), ex situ secondary ion mass spectrometric analysis (12 kV Ga+ primary ion beam), and through X-ray photoelectron spectroscopy by monitoring Si (2s). The nature of the surface modification was further established by analysis of synthetic SAM surfaces made up of mixtures of the trimethylsilyl-11-mercapto-1-undecane ether and various proportions of the hydroxyl-terminated mercaptan (11-mercapto-1-undecanol). These mixed surfaces, as well as the spectroscopic data, indicate that ca. 30% of the hydroxyl chains are covalently modified at saturation coverage. Analogous surface transformations are achieved using Si(CH3)2F+ and Si(CH3)2C6H5+.