Novel [polymer]/[organically modified silicon oxide (ORIMOSIL)] hybrids were formulated via sol-gel reactions of mixtures of tetraethoxysilane (TEOS) and diethoxydimethylsilane (DEDMS) in the nanophase-separated morphology of perfluorosulfonic acid (PFSA) films. Molecular structures of ORMOSIL phases were investigated by FT-IR spectroscopy and the spectra compared with those of corresponding bulk ORMOSILs. Spectra are similar for PFSA in situ and bulk ORMOSILs, suggesting that short-range molecular structures in the two states are in fact comparable. Spectral trends with ORMOSIL composition suggest that similar D, Q sequence distributions exist for the two systems. There is evidence of co-condensation between Q and D units within the PFSA, as well as in the bulk ORMOSILs. As DEDMS:TEOS increases, ORMOSIL structures in both in situ and bulk states are increasingly more linear. It appears that a spectrum of energetic environment, or polarity, in the clusters of perfluorosulfonate ionomers can be tailored by adjusting the ratio of Si-OH and Si-CH3 groups in ORMOSIL nanophases.