Self-assembled monolayers of alkyl phosphonic acids on anodic aluminum oxide (AlOx) surfaces are important as dielectric layers in thin film electronic devices. Assessing the properties and quality of these monolayers on amorphous AlOx is limited to a few surface-sensitive methods. In this work, we study using nonlinear optical measurements the molecular ordering in n-alkyl phosphonic acids with various alkyl chain lengths (6 to 18 carbons) deposited on AlOx and show the influence of temperature on stability and conformational order. The results demonstrate that the octadecylphosphonic acid has fewest defects in the chain orientation. A detailed comparison of the longest and the shortest alkyl chain revealed different behavior in conformational ordering upon annealing.