The interaction of vapor-deposited Al atoms with self-assembled monolayers (SAMS) of HS(CH2)(16)-X (X = -OH and -OCH3) chemisorbed at polycrystalline Au 1111 surfaces was studied using time-of-flight secondary-ion mass spectrometry, X-ray photoelectron spectroscopy, and infrared reflectance spectroscopy. Whereas quantum chemical theory calculations show that Al insertion into the C-C, C-H, C-O, and O-H bonds is favorable energetically, it is observed that deposited Al inserts only with the OH SAM to form an -O-Al-H product. This reaction appears to cease prior to complete -OH consumption, and is followed by formation of a few overlayers of a nonmetallic type of phase and finally deposition of a metallic film. In contrast, for the OCH3 SAM, the deposited Al atoms partition along two parallel paths: nucleation and growth of an overlayer metal film, and penetration through the OCH3 SAM to the monolayer/Au interface region. By considering a previous observation that a CH3 terminal group favors penetration as the dominant initial process, and using theory calculations of Al-molecule interaction energies, we suggest that the competition between the penetration and overlayer film nucleation channels is regulated by small differences in the Al-SAM terminal group interaction energies. These results demonstrate the highly subtle effects of surface structure and composition on the nucleation and growth of metal films on organic surfaces and point to a new perspective on organometallic and metal-solvent interactions.