Adverse conditions caused by abiotic stress modulate the plant development and growth by altering some morphological and cellular mechanisms. To face this problem, plants, along with physiological adaptations, developed intracellular mechanisms, including changes in protein production and trafficking or modifications of the endomembrane system. Protein trafficking within the cell involves innumerous complexes and receptors that has been characterized along the years. For this study, some were selected based on their role and localization within the endomembrane system: BP-80, responsible for vacuolar sorting at the trans-Golgi and PVC levels; VTI12 works in the vacuolar pathway; SYP121 and SYP23, which mediate the vesicle trafficking from Golgi and Endoplasmic Reticulum membrane; SYP51, a SNARE involved in post-Golgi membrane trafficking to the tonoplast; VAMP, a vesicle associated membrane protein; RMR1, a transmembrane receptor; and EXO70, a subunit from exocist. The Plant Specific Insert (PSI) is a domain present in some aspartic proteinases that modulates their trafficking to the vacuole in a non-conventional way, bypassing the Golgi. It is known that stress situations can alter protein sorting to the vacuole, changing their routes via a Golgi-independent pathway. Our goal is to evaluate the expression levels of different aspartic proteinases and respective PSIs, and well-characterized genes involved in the vacuolar pathway. A.thaliana seedlings were germinated in Murashige and Skoog medium supplemented with excess of mannitol (osmotic stress), hydrogen peroxide (oxidative stress), excess of sodium chloride (saline stress) or sub-lethal doses of zinc sulfate (heavy metals stress) The expression analysis of the genes under study was performed by qPCR after RNA extraction from seedlings. The results obtained point to a different response of the three aspartic proteinases under study: PSI1, which is upregulated in all the stress situations, excluding the heavy metal; PSI2, that is downregulated for the oxidative stress; and PSI3 that is upregulated for the saline stress and downregulated for the zinc stress. ​These results indicate that different, yet related, aspartic proteinase genes respond differently to different types of stress, indicating a fine-tuned regulation. Furthermore, our results regarding the endomembrane system effectors show us that EXO70, RMR1, SYP51, SYP121 and VTI12 are up regulated in all the stress conditions, while VAMP, SYP23 and BP80 are downregulated in the same situations. This demonstrates that adverse conditions caused by abiotic stress can alter the expression of key proteins involved in the protein trafficking machinery, which can be related with the activation/deactivation of certain pathways, important for plant tolerance to stress.