In this work different synthesis routes were evaluated with the aim of optimizing the incorporation of niobium within a hybrid silica matrix on an atomic scale. The fast kinetics of the hydrolysis/polycondensation of the organic Nb precursor Nb(OEt)5 entails a segregation of the resulting material into Nb2O5 and a silica based network. To overcome this effect we (a) performed a prehydrolysis of 1,2-bis-triethoxy-ethane (BTESE) prior to adding niobium penta-ethoxide, or (b) attempted to reduce the availability of Nb via a complexation of Nb by either acetylacetone or 2-methoxyethanol. The network organization was evaluated from results of Fourier transform infrared as well as 13C, 29Si and 17O MAS NMR spectroscopy. Whereas the prehydrolysis of BTESE and the addition of 2-methoxyethanol induced only moderate mixing of Nb and Si, leading to a network in which islands of Nb2O5 are linked to the hosting silica based matrix via Nb–O–Si bonds, the use of acetylacetonate lead to a mixing of Nb and Si on the atomic scale, forming a mixed Nb–O–Si network without any extended clusters of segregated Nb2O5. The Si–C–C–Si bridge from the silsesquioxane is found to survive the condensation process and is even present in the resulting materials after annealing at 200 °C.