Self-assembled monolayers (SAMs) of alkanephosphonic acids with chain lengths between 8 and 18 carbon units were formed on thin films of indium tin oxide (ITO) sputter-deposited on silicon substrates with 400 nm thermally grown SiO(2). The silicon substrates, while not intended for use in near-IR or visible optics applications, do provide smooth surfaces that permit systematic engineering of grain size and surface roughness as a function of the sputter pressure. Argon sputter pressures from 4 to 20 mTorr show systematic changes in surface morphology ranging from smooth, micrometer-sized grain structures to <50 nm grains with 3 x higher surface roughness. Near-edge X-ray absorption fine structure (NEXAFS) spectroscopy experiments are conducted for alkanephosphonic acids deposited on these wide range of ITO surfaces to evaluate the effects of these morphological features on monolayer ordering. Results indicate that long-chain SAMs are more highly ordered, and have a smaller tilt angle, than short-chain SAMs. Surprisingly, the 1-octadecyl phosphonic acids maintain their order as the lateral grain dimensions of the ITO surface shrink to similar to 50 nm. It is only when the ITO surface roughness becomes greater than the SAM chain length (similar to 15 angstrom) that SAMs are observed to become relatively disordered.