This work studied the solvent-free sol–gel process of (3-glycidyloxypropyl)trimethoxysilane using three different experimental setups and a ternary amine (DABCO) or a tin-based compound (DBTL) as the sol–gel catalysts, which allowed to prepare homogeneous liquid products and control their final microstructures. The aim was to synthesize epoxy-functionalized precursors for hybrid epoxy-based materials. The NMR spectroscopy, MALDI-TOF, DLS, FTIR and SEC were used to characterize the obtained sols and xerogels. The formed silica structures were primarily dependent on the type of catalyst used, but small cyclic structures were always present. Nevertheless, the DABCO-catalyzed system showed a higher tendency to create cage-like structures in contrast to the system that used DBTL catalyst in which larger ladder-like structures prevailed. The sols as well as the final xerogels with the higher condensation degree of alkoxysilane bonds were prepared under the basic (DABCO) conditions. All prepared liquid products (sols) were well miscible with epoxy pre-polymers and therefore can be considered as suitable epoxy-functionalized precursors for preparation of hybrid materials based on epoxy matrix.