AbstractIn the plant development cycle, different types of proteases play essential functions. Plant vacuolar processing enzymes (VPEs) are a group of cysteine proteases localized in the cell vacuoles that process and regulate several larger proprotein precursors. VPEs activate the proteolytic cleavage of proproteins precursors within aspartic acid and asparagine residues to trigger the tightly controlled programmed cell death process induced by different stages of plant development and environmental cues, impacting myriad plant physiological processes. In plants, VPEs are categorized into embryo, vegetative, and seed coat‐types, in which embryo and seed coat‐type VPEs are mainly involved in processing the seed storage protein precursors to provide nutrients for early growth, while the vegetative type induces programmed cell death in a varied range of vegetative tissues. Recently, several plant VPEs exhibited transpeptidase activity, which is essential for the cyclization mechanism during the production of cyclotides. In this review, we explore and understand the complex functions of plant VPEs, which can lead to the production of stress‐tolerant and higher‐yield crops, and provide the recent advances in the application of VPEs in molecular pharming, which highlights the significant implications of VPEs in protein science and agriculture.