The epoxy-silica hybrids have been prepared by the non-aqueous sol–gel process and the in situ generation of nanosilica from tetraethoxysilane was initiated with borontrifluoride monoethylamine (BF3MEA). The DGEBA based epoxy networks with aliphatic, cycloaliphatic and aromatic amines were used as matrices. The solventless technique made it possible to avoid drawbacks of the classical aqueous procedure. The “non-aqueous” systems show improved homogeneity and thermomechanical properties in particular at the application of the coupling agent glycidyloxypropyl trimethoxysilane. Mechanism of the non-aqueous sol–gel process under BF3MEA action and evolution of the hybrid structure during polymerization, followed by chemorheology, are discussed. The nanosilica structure growth is slower under the non-aqueous procedure thus facilitating a better structure control. The hybrids with both particulate and bicontinuous morphologies were prepared and the epoxy-silica interphase bonding and crosslinking through the formed silica domains was proved. The hybrid hierarchical structure and morphology were determined by NMR, SAXS, TEM and DMA.