The evolution of structure in sol–gel derived mixed bridged silsesquioxane-niobium alkoxide sols and drying thin films was monitored in situ by small-angle X-ray scattering. Since sol–gel condensation of metal alkoxides proceeds much faster than that of silicon alkoxides, the incorporation of d-block metal dopants into silica typically leads to formation of densely packed nano-sized metal oxide clusters that we refer as metal oxide building blocks in a silica-based matrix. SAXS was used to study the process of niobia building block formation while drying the sol as a thin film at 40–80 °C. The SAXS curves of mixed niobia-hybrid silica sols were dominated by the electron density contrast between sol particles and surrounding solvent. As the solvent evaporated and the sol particles approached each other, a correlation peak emerged. Since TEM microscopy revealed the absence of mesopores, the correlation peak was caused by a heterogeneous system of electron-rich regions and electron poor regions. The regions were assigned to small clusters that are rich in niobium and which are dispersed in a matrix that mainly consisted of hybrid silica. The correlation peak was associated with the typical distances between the electron dense clusters and corresponded with distances in real space of 1–3 nm. A relationship between the prehydrolysis time of the silica precursor and the size of the niobia building blocks was observed. When 1,2-bis(triethoxysilyl)ethane was first hydrolyzed for 30 min before adding niobium penta-ethoxide, the niobia building blocks reached a radius of 0.4 nm. Simultaneous hydrolysis of the two precursors resulted in somewhat larger average building block radii of 0.5–0.6 nm. This study shows that acid-catalyzed sol–gel polymerization of mixed hybrid silica niobium alkoxides can be rationalized and optimized by monitoring the structural evolution using time-resolved SAXS.