Hybrid organically linked silica is a highly promising class of materials for the application in energy-efficient molecular separation membranes. Its high stability allows operation under aggressive working conditions. Herein is reported the tailoring of the separation performance of these hybrid silica membranes by adjusting the size, flexibility, shape, and electronic structure of the organic bridging group. A single generic procedure is applied to synthesize nanoporous membranes from bridged silsesquioxane precursors with different reactivities. Membranes with short alkylene (CH2 and C2H4) bridging groups show high H2/N2 permeance ratios, related to differences in molecular size. The highest CO2/H2 permeance ratios, related to the affinity of adsorption in the material, are obtained for longer (C8H16) alkylene and aryl bridges. Materials with long flexible alkylene bridges have a hydrophobic surface and show strongly temperature-dependent molecular transport as well as a high n-butanol flux in a pervaporation process, which is indicative of organic polymerlike properties. The versatility of the bridging group offers an extensive toolbox to tune the nanostructure and the affinity of hybrid silica membranes and by doing so to optimize the performance towards specific separation challenges. This provides excellent prospects for industrial applications such as carbon capture and biofuel production.