A molecular-scale investigation of the interaction at room temperature between gaseous trichlorosilane (HSiCl3), used as a passivating agent, and surfaces of aluminum alloy AA6061 in a polished or hydroxylated state is conducted. Atomic force microscopy (AFM) and scanning electron microscopy (SEM) provide information on the topography and morphology of AA6061 before and after hydroxylation and surface passivation, while surface chemistry has been investigated by Polarization Modulation Infrared Reflection-Absorption Spectroscopy (PM-IRRAS) and X-ray photoelectron spectroscopy (XPS). Oxidation and hydroxylation of the polished alloy surface in boiling water strongly modifies the roughness of the surface, with formation of platelets and needles of oxyhydroxide AlOOH. PM-IRRAS and XPS reveal that, upon adsorption, HSiCl3 dissociates and mainly forms HSiOHn(OAl)3−n, HSi(OSi)n(OAl)3−n and condensed HSiOx species, by reaction with single bondOH groups from the AlOOH surface phase. The amount of deposited Si-containing species is larger on the rough surface of the hydroxylated alloy and this deposit is accompanied by a decrease of the amount of free single bondOH groups evidenced by PM-IRRAS. These results can find applications in the field of functionalization of aluminum alloys. It is suggested that a homogeneous oxidation of the alloy surface prior to exposure to gaseous HSiCl3 may enhance the adsorption of the passivating agent.