Grapevine is a large source of healthy polyphenols for human diet, and red table-grapes and wines are the main source of stilbenes. These compounds are important both in the plant defence system and for human health. In the present study, Vitis vinifera cv. Barbera cell cultures were treated with 50 µg/mL chitosan and proteomic analyses on soluble and membrane subcellular fractions were performed against suitable controls. Three soluble stilbene synthase protein spots, four stilbene synthase spots in the microsomal fraction and four spots of membrane ATPase subunits were identified, the accumulation of which was modulated in response to chitosan treatment. Present proteomic and immunolocalisation data seem to provide evidence supporting the hypothesis that a stilbene biosynthetic multi-enzyme complex is associated with the intracellular membrane. In addition, proteomic analyses showed a general decrease in the accumulation of proteins belonging to different primary metabolism pathways, both in the soluble and membrane fractions. In particular, energy, sugar and amino acid metabolisms were down-regulated as a consequence of chitosan and acetic acid treatments. These metabolic modifications could lead to a consistent change in the profile and amount of metabolites stored in grape berries, with consequent effects on taste, flavour, organoleptic and nutraceutical properties of derived food products.