Rubber–silica nanocomposites containing 10 wt % silica were prepared using in situ hydrolysis and condensation of tetraethyl orthosilicate (TEOS) in the presence of n-hexylamine as catalyst in two rubber matrices, namely, natural rubber and ethylene-propylene diene rubber. The structure of sol–gel synthesized silica, mapped by solid-state NMR spectroscopy and XPS, indicated the presence of remnant ethoxy groups inside the silica particles and on the silica surface, while hexylamine resided preferentially at the silica surface stabilized via hydrogen bonding of the ethoxy and chemisorption of the hexylamine. Thus, the preparation of sol–gel synthesized silica results in the formation of so-called "hairy" silica particles with increased hydrophobic properties. The combinatory technique FTIR-TGA-MS confirms the complex chemistry of the sol–gel synthesized silica as well as the low amount of residual ethanol present in the particles and the in situ rubber–silica nanocomposite, the latter aspect being important when industrial manufacturing and application of in situ rubber–silica nanocomposites is considered. It is further shown that (i) the particular surface chemistry, (ii) the phenomena of entrapped rubber chains inside the silica nanoparticles, and (iii) morphology of the sol–gel synthesized silica nanoparticles lead to a more intimate interaction with the rubber matrix, which may be fine-tuned toward improved mechanical properties.