Adverse conditions caused by abiotic stress modulate plant development and growth by altering 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. 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 well-characterized genes involved in the vacuolar pathway, in plants submitted to different abiotic stresses (osmotic, oxidative, saline and heavy metals). The results obtained point to a different response of the three aspartic proteinases under study, indicating that different, yet related, genes respond differently to different types of stress, resulting in a fine-tuned regulation. Furthermore, our results regarding the endomembrane system effectors show that AtEXO70, AtRMR1, AtSYP51, AtSYP121 and AtVTI12 are up-regulated, while AtVAMP, AtSYP23 and AtBP80 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 to the activation/deactivation of certain pathways.