In eukaryotes, the endomembrane system allows for spatiotemporal compartmentation of complicated cellular processes. The plant endomembrane system consists of the endoplasmic reticulum, the Golgi apparatus, the trans-Golgi network, the multivesicular body and the vacuole. Anterograde traffic from the endoplasmic reticulum to the Golgi apparatus is mediated by coat protein complex II (COPII) vesicles. Autophagy, an evolutionarily conserved catabolic process that turns over cellular materials upon nutrient deprivation or in adverse environments, exploits double-membrane autophagosomes to recycle unwanted constituents in the lysosome/vacuole. Accumulating evidence reveals novel functions of plant COPII vesicles in autophagy and their regulation by abiotic stresses. Here, we summarize current knowledge about plant COPII vesicles in endomembrane trafficking and then highlight recent findings showing their distinct roles in modulating the autophagic flux and stress responses.