This study presents a sustainable method to purify stilbenes from residual grape stem biomass. This approach was experimentally validated through the use of a pilot size fixed-bed adsorption prototype for the automation of the purification process. Molecularly imprinted polymers, synthesized through photopolymerization at room temperature and incorporating the 4-vinylpyridine monomer, serve as adsorbents. The purification procedure leads to a significant enrichment, with a more than 22-fold increase in (E)-ε-viniferin and a 9-fold increase in (E)-resveratrol. High recoveries of 80.3% and 62.1% for (E)-ε-viniferin and (E)-resveratrol, respectively, were achieved. Notably, the use of eco-friendly water and ethanol mixtures distinguishes this method from others focused on stilbenes purification. This study further explores the variability of the stilbenes in the residual grape stems by analysing different varieties, emphasizing the complexity of the starting material of the purification process. The range of purities achieved for the fractions enriched with stilbenes (e.g., 12.8% for (E)-ε-viniferin and 3.4% for (E)-resveratrol) are suitable for direct use in controlling of Plasmopara viticola, the agent causing grapevine downy mildew. Furthermore, through compositional combination of these fractions, it is possible to conceive new stilbene-containing phytochemicals with improved anti-fungal activity. Therefore, the developed adsorbents and purification process, enabling the steady enrichment of stilbenes regardless of the unavoidable variability in the initial vine biomass, is a contribution towards the quest for more environmentally friendly and sustainable phytochemicals.