Microwave flash annealing dramatically enhances the environmental stability of AuCl3-doped single-walled carbon nanotube (SWCNT) films on plastic substrates using fast microwave nanoheating to produce a large temperature difference between the films and the substrates. Within one second, the microwave nanoheating rapidly caused thermal decomposition of AuCl3 dopants as well as simultaneous embedding of SWCNTs in the substrate, without deforming it. The hygroscopic Cl atoms were partially desorbed from the SWCNTs by rapid thermal decomposition, and the embedded substrate surface acted as a passivation layer, which synergistically contributed to the stability of the doped and annealed SWCNTs.