Treatment with triethoxyfluorosilane (TEFS) enhances the hydrophobic properties of high-silica MFI and MEL membranes synthesized by a microwave-assisted secondary growth method. The modified membranes showed significant improvement in recovery of ethanol from ethanol/water mixtures by pervaporation. The TEFS treatment was also able to heal some intercrystalline defects in the zeolite membrane film. Additional physical–chemical characterization revealed that the external zeolite surface is selectively covered by the organosilane without blocking zeolite micropores. The grafted Si–F moieties are thermally and hydrothermally stable.