The epoxidation of cyclohexene over titania–silica aerogel catalysts using t-butylhydroperoxide (TBHP) was investigated by in situ attenuated total reflection (ATR) infrared spectroscopy. In order to distinguish between relevant and spectator species and to increase sensitivity, ATR was combined with modulation spectroscopy. In the latter technique the catalyst system is periodically perturbed by a forced concentration change. The interaction of cyclohexene with the aerogels is found to be weak. In contrast, TBHP adsorbs strongly on the catalysts on two different sites. Modulation experiments reveal that TBHP adsorbed on Si-OH groups is a spectator, whereas the one adsorbed on the Ti-sites is involved in the catalytic cycle. The latter species is stronger adsorbed and the associated signals increase with the Ti content of the catalyst. Adsorption of the TBHP on the Ti sites results in a strong shift of the C-O stretching vibration and changes in the Ti-O-Si modes of the catalyst. The study furthermore reveals vastly different pore diffusion for cyclohexene and TBHP due to their different interaction with the polar catalyst surface. In the modulation experiments the reaction product appears retarded with respect to the admittance of the reactants, which indicates that pore diffusion and kinetics of adsorption and desorption are important factors for the catalysis. Methylation of the aerogel has a beneficial effect on the catalysis, which can be traced to the different pore size distribution and polarity with respect to the unmodified catalyst. When the flow-through ATR cell is slowly heated, a change in the framework vibrations of the catalyst occurs simultaneously with the onset of reaction, indicating reaction induced structural changes.