In the current study, extracellular vesicles from pomegranate juice (PgEVs) were isolated for the first time using size exclusion chromatography (SEC). This method permitted us to obtain highly enriched EV samples without most of the non-EV co-isolated proteins. The characterization of PgEVs through nanoparticle tracking analysis (NTA) and transmission electron microscopy (TEM) allowed the determination of vesicles' concentration/volume, size, and morphology. It was confirmed from the analytical data that PgEVs contain a homogeneous population of vesicles, with a dimension and structure comparable to plant-derived EVs. Proteomic analyses by LC-MS/MS led to the characterization of 131 proteins, and several of them were related commonly to the biogenesis and transport of EVs, and/or proposed as EV markers. PgEVs exerted anti-inflammatory, antioxidant and wound-healing effects when added to the in vitro cultures of monocytic (THP-1) and intestinal (Caco-2) cell lines, respectively.