Functionalization of Aluminium surfaces by phosphonic acid (PA) treatments is of key industrial importance. This work discloses the effect of PA molecular design on the performance of aqueous PA surface treatments of Aluminium under acidic conditions. Comprehensive XPS and ToF-SIMS analyses show that the “final” nature of the PA adsorbate layer is not only governed by competing in-situ PA adsorption and oxide dissolution processes, but also by modifications of the transient state of the adsorbate layer during subsequent water rinsing in air. Low-soluble organo-metallic-phosphonic (OMP) deposits formed by complexation with Al3+ ions in solution are largely removed upon water-rinsing; only few physisorbed OMP complexes are converted trans-situ to a chemisorbed state. The in-situ oxide dissolution and ex-situ re-oxidation processes are suppressed with increasing steric size of the PA molecule. Moreover, intermolecular phenyl π-π interactions can act as a driving force to increase the surface density of the PA adsorbate layer in-situ, which also effectively suppresses in-situ oxide dissolution and ex-situ re-oxidation. The findings provide profound insights on how PA molecular designs can be tuned to tailor the chemistry and morphology of PA-adsorbate layers, which may contribute to advance surface treatment strategies of Al surfaces for a wealth of applications.