Commercial application of zeolite membranes has been hindered by the challenge of preparing defect-free membranes. Herein, we report a facile method able to selectively plug grain boundary defects in high-flux MFI zeolite membranes by coking of iso-propanol at 350 °C. After modification, the permeance via defects was reduced by 70%, whereas that via zeolite pores was reduced by only 10%.