Membrane vesicles isolated from vegetable tissues have shown promise in encapsulation technologies used in industries like food and cosmetics, offering innovative approaches to product development. However, their associated linked metabolites have not been studied. Lemon vesicle research not only adds value to the lemon crop (Citrus × limon L.), one of the most widely cultivated fruit trees in the world, is a source of bioactive compounds such as phenolics and organic acids. In this study, the influence of elicitation with ZnSO₄ and methyl jasmonate, which modulate the bioactive metabolites, on fruit membrane vesicle bond metabolites was studied. The study showed that foliar application of ZnSO₄ increased phenolic compounds as caffeic, sinapic, and chlorogenic acids and the flavonoid hesperidin by about 20% in lemons. Furthermore, a clear interaction between vesicles and citrate and ascorbate that were increased by methyl jasmonate were associated with their higher bioactivity. This was related to the double intrinsic in vitro antioxidant activities of these vesicles.