The growth of self-assembled monolayers from octadecyltrichlorosilane (OTS) on modified silicon surfaces has been investigated. The influence of different immersion times in a deactivation reagent on the growth mechanism and the ordering of the films has been studied. Characterization of the films and the submonolayer coverage has been performed with tapping mode atomic force microscopy, ellipsometry, and infrared spectroscopy. We found that a deactivation of active sites led to a higher mobility of adsorbed molecules on the surface resulting in circular islands of highly ordered alkylsiloxane. However, upon prolonged immersion in OTS these ordered islands did not continue to grow and full monolayer coverage could not be obtained. Instead, an exchange reaction with the deactivation reagent leading to a disordered film between the ordered islands was observed. This was confirmed by external reflection infrared spectroscopy.