Natural deep eutectic solvents (NADES) based on choline chloride and organic acids were applied for the recovery of phenolic compounds from three agro-industrial residues: pomegranate peels, almond hulls, and elderberry pomace. Box-Behnken designs were conducted to reach the best extraction conditions, which were 50 degrees C, 20 min, and 20 w/w NADES/solid for pomegranate peels, 30 degrees C, 60 min, and 20 w/w NADES/solid for almond hulls, and 40 degrees C, 60 min, and 30 w/w NADES/solid for elderberry pomace. Punicalagin was the major phenolic in the NADES-based pomegranate extract, with a concentration about 87% higher than that found in the ethanolic extract obtained under the same conditions. The same was valid for (+)-catechin, a major phenolic in almond extracts, and cyanidin-3-sambubioside, a major anthocyanin in elderberry extracts, with concentrations around 27 and 68% higher in the NADES extracts, respectively. These findings show that the extraction of valuable compounds from agro-industrial waste using NADES was improved with accuracy during ultrasound-assisted extractions.