The attachment chemistry required for the sequential self-assembly of zirconium phosphonate (ZP) monolayers on gold and germanium surfaces is examined with a combination of attenuated total reflection (ATR-FTIR) and polarization modulation (PM-FTIR) Fourier transform infrared spectroscopies. On the germanium substrates, the conversion of an attached omega-aminosilane monolayer to phosphate amide species creates a primer for the sequential deposition of multilayer films of zirconium 1,10-decanediylbis-(phosphonate)(Zr/DBP). On vapor-deposited gold films, a packed monolayer of 11-mercapto-1-undecanol (MUD) serves as the basis for a primer monolayer. PM-FTIR measurements show that phosphorylation of the terminal hydroxy groups results in a surface with a mixture of phosphate mono- and diesters, which bind Zr4+ to commence the self-assembly of the Zr/DBP multilayers. On both substrates, the alkyl chain regions of the ZP film are observed to be conformationally disordered due to the control of the lateral spacing in the films by the inorganic (phosphonate-Zr-phosphonate) regions. Furthermore, the packing density, order, and chemical structure of the primer layer are found to influence the resulting ZP multilayer structure.