Vine shoots are the main by-products of grapevine pruning with no added value. In the present study, deep eutectic solvents (DESs) were used as alternatives to traditional chemical solvents, for the extraction of phytochemicals from grapevine shoots. Three levulinic acid-based DESs were tested for the first time, and their performance was compared to methanol (a standard chemical solvent) regarding the extraction of phenolic compounds from thirteen Vitis sp. shoots. Two extraction methods have been applied: ultrasound-assisted extraction and solid-liquid extraction. A total of eleven polyphenols which belongs to four families (proanthocyanins, stilbenes, hydroxycinnamic acids, and flavonols) have been identified and quantified in the extracts. The statistical analysis shows that the levulinic acid-based DES systems are novel and important alternatives to chemical solvents due to favourable eco-friendly properties and remarkable extraction performance of polyphenols. On the other hand, the ultrasound-assisted extraction technique has significantly increased the extraction rate in comparison to the solid-liquid extraction method with p-values lower than 0.05 for most compounds. The genetic factor has been shown to play an important role in the content of extracted polyphenols, being V. riparia pubescente the one that presented the highest concentrations of extracted polyphenols. Finally, the polyphenol-enriched extracts have proven important properties such as antioxidant activity and significant delay in bacteria growth against both gram-positive and gram-negative bacteria. It is important to note that, to the best of our knowledge, this is the first time that deep eutectic solvents have been used for the extraction of bioactive compounds from vine shoot residues.