Protein sorting is an essential biological process in all organisms. Trafficking membrane proteins generally relies on the sorting machinery of the Golgi apparatus. However, many proteins have been found to be delivered to target locations via Golgi-independent pathways, but the mechanisms underlying this delivery system remain unknown. Here, we report that Sec24C mediates the direct secretory trafficking of the phytochelatin transporters ABCC1 and ABCC2 from the endoplasmic reticulum (ER) to prevacuolar compartments (PVCs) in Arabidopsis thaliana. Genetic analysis showed that the sec24c mutants are hypersensitive to cadmium (Cd) and arsenic (As) treatments due to mislocalisation of ABCC1 and ABCC2, which results in defects in the vacuole compartmentalisation of the toxic metals. Furthermore, we found that Sec24C recognises ABCC1 and ABCC2 through direct interactions to mediate their exit from the ER to PVCs, which is independent of brefeldin A-sensitive post-Golgi trafficking pathway. These findings expand our understanding of Golgi-independent trafficking, which also provide key insights regarding the mechanism of tonoplast protein sorting and open a new perspective on the function of Sec24 proteins.