Sambucus nigra flowers, known as elderberry flowers (EBF), are a plant tissue rich in polyphenolic phytochemicals with important bioactivities. However, there are few studies dealing with the production of polyphenol-containing EBF extracts. The objective of the investigation presented herein was the development of a high-performance green extraction methodology, to generate EBF extracts enriched in polyphenolic substances, using an efficient deep eutectic solvent, combined with ultrasonication pretreatment. The DES was composed of L-lactic acid (hydrogen bond donor—HBD) and glycine (hydrogen bond acceptor—HBA) and, after an initial screening to properly regulate HBD/HBA ratio, the extraction was optimized by deploying response surface methodology. Under the optimized conditions, which were DES/water (85% w / v ), liquid-to-solid ratio 60 mL g−1, and stirring speed 200 rounds per minute, the extraction yield in total polyphenols amounted to 121.24 ± 8.77 mg gallic acid equivalents per g dry matter. The integration of ultrasonication prior to the batch stirred-tank extraction boosted polyphenol recovery of up to 174.73 ± 2.62 mg gallic acid equivalents per g dry matter. Liquid chromatography–mass spectrometry analysis showed that the richest EBF extract obtained was dominated by rutin, a di-p-coumaroylquic acid and chlorogenic acid.