Sequential processing of multiply functionalized mesoporous films is shown to yield materials that are compositionally and structurally heterogeneous on mesoscopic and molecular length scales, both of which must be controlled to optimize macroscopic ion-conduction properties. Cubic mesoporous silica films prepared from strongly acidic solutions were subsequently functionalized under highly alkaline conditions to incorporate hydrophilic aluminosilica surface moieties, followed by nonaqueous conditions to introduce perfluorosulfonic-acid surface groups. Such sequential combination of individually incompatible steps yielded stable mesoporous films with high surface hydrophilicities and strong acid functionalities that exhibited high proton conductivities (ca. 9 × 10(-2) S/cm) at elevated temperatures (120 °C). Molecular, mesoscopic, and macroscopic properties of the multiply functionalized films were monitored and correlated at each stage of the syntheses by nuclear magnetic resonance (NMR) spectroscopy, small-angle X-ray scattering (SAXS), transmission electron microscopy (TEM), elemental analysis, adsorption, and ion conductivity measurements. In particular, variable-temperature solid-state two-dimensional (2D) (27)Al{(1)H}, (29)Si{(1)H}, (27)Al{(19)F}, and (29)Si{(19)F} HETeronuclear chemical-shift CORrelation (HETCOR) NMR spectra reveal separate surface adsorption and grafting sites for the different functional surface species within the mesopore channels. The hydrophilic aluminosilica and acidic fluoro-group loadings and interaction sites are demonstrated to be strongly affected by the different synthesis and functionalization treatments, which must be separately and collectively optimized to maximize the proton conductivities.