The sol-gel synthesis of a silica based ionogel using the ionic liquid 1-hexyl-3-methylimidazolium bis(trifluoromethanesulfonyl)imide (C6C1ImTFSI) as the solvent has been followed in situ by combined μ-focused X-ray scattering and μ-Raman spectroscopy. By covering the momentum transfer range 0.2 < q < 30 nm(-1) we probe the evolution of the characteristic peaks of the ionic liquid, associated with the existence of polar and non-polar domains, as a function of reaction time. Our detailed analysis of the small angle X-ray scattered (SAXS) pattern reveals that the nano-structure of the ionic liquid is partially retained during the sol-gel synthesis, as indicated by the broader yet distinguishable SAXS signatures. We also observe that the signature associated with the non-polar and polar domains shift to higher and lower q-values, respectively. Interestingly, this behavior correlates with the evolution of the chemical composition of the sol as probed by Raman spectroscopy. More precisely, we observe that both the nano-structural changes and the production of polar molecules arrest at the point of gelation. This is rationalized by the tendency of the reagents and products of the sol-gel reaction to locate in different portions of the nano-structure of the ionic liquid.