It is quite challenging to avoid microdefect formation during hydrothermal growths and/or calcination processes, while manufacturing high-quality zeolite membranes in a reproducible manner. Even less than 1% of defects, which generally provide nonselective pathways, will considerably worsen the intrinsic, high molecular sieving-based separation performance of a continuous zeolite membrane. Herein, we propose a simple and reliable method for blocking defects using water-soluble dye molecules, which were originally used for the visualization of nonzeolitic, defective structures in a zeolite membrane. Because the dye molecules are ∼1 nm in size, they cannot diffuse into the zeolitic pores and selectively access the defects. For the demonstration of dye-based defect healing, we chose a siliceous chabazite type SSZ-13 zeolite membrane (pore size = 0.37 × 0.42 nm 2 ) with some degree of defects and investigated the effect of defect healing on the final CO 2 separation performance. Because the defects were gradually filled by the dye molecules, both CO 2 /N 2 and CO 2 /CH 4 separation performances were concomitantly increased. Intriguingly, the CO 2 permselectivity test with ternary mixtures including H 2 O vapor (the third largest component in the flue and natural/shale/bio gas streams) in the feed diminished CO 2 separation performance. This could be ascribed to inhibited transport of the fast permeating species, here CO 2 , from the adsorbed H 2 O molecules on the dye-treated and water-friendly (relatively hydrophilic) membrane surface. On the contrary, the intact, siliceous (water-repelling or hydrophobic) SSZ-13 membranes showed improved CO 2 permselectivities in the presence of H 2 O vapor, seemingly due to defect blocking by the physisorbed H 2 O molecules.