Al atom deposition with controlled coverages has been carried out on self-assembled monolayers (SAMS), prepared by assembly of HS(CH2)(15)X, with X = -CH3 (M-SAM) and -CO2CH3 (ME-SAM), on Au {111} substrates, and the resulting structures and electrical properties analyzed in situ by ultrahigh-vacuum, multiple mode atomic force microscopy (contact, noncontact, and conducting probe) and infrared reflection spectroscopy. The M-SAM data clearly reveal a distinct morphology transition at similar to 3 Al atoms per adsorbate molecule (3 EL) from formation of a buried similar to 1:1 Al-Au adlayer at low coverages to metal overlayer cluster nucleation and the appearance of isolated metal nanofilaments; with varied behaviors including Ohmic conduction, resistive switching (memristor), and vestiges of quantum-like conductance steps. The ME-SAM data confirm our earlier report of a highly efficient, 1:1 chemical trapping of initial nascent Al atoms by the terminal ester group while also revealing formation of isolated, conducting filaments, mainly at SAM defects, and the presence of an insulating overlayer up to similar to 5 EL. For both SAMS, despite the large thermochemical driving forces to exhaustively form inorganic products, subtle kinetic pathways guide the evolution of metal nanostructures within and contiguous to the SAM. Overall the experiments demonstrate a highly controlled, quantitative strategy for exploring the chemistry of nascent metal atoms with organic moieties as well as providing opportunities to generate novel metal nanostructures with significant implications for molecular and organic device applications.