The synthesis of nanostructured zeolites enables modification of catalytically relevant properties such as effective surface area and diffusion path length. Nanostructured zeolites may be synthesized either in alkaline media, and so contain significant numbers of hydrophilic silanol groups, or in expensive and harmful fluoride-containing media. Here, we report and characterize, using a combination of experimental and theoretical techniques, the one-pot synthesis of silanol-free nanosized MFI-type zeolites by introducing atomically dispersed tungsten; this prevents silanol group occurrence by forming flexible W-O-Si bridges. These W-O-Si bonds are more stable than Si-O-Si in the all-silica MFI zeolite. Tungsten incorporation in nanosized MFI crystals also modifies other properties such as structural features, hydrophobicity and Lewis acidity. The effect of these is illustrated on the catalytic epoxidation of styrene and separation of CO2 and NO2. Silanol-free nanosized W-MFI zeolites open new perspectives for catalytic and separation applications.