For the isolation of selected phenolic compounds from dried chokeberries, natural deep eutectic solvents (NADESs) were investigated as a green alternative to conventionally used extraction solvents. Four types of NADESs were synthesised, with choline chloride as the hydrogen bond acceptor in combination with different hydrogen bond donors (sugars, organic acid and urea). Ultrasound-assisted extraction was used to improve the extractability of the phenolic compounds and the results were compared to those obtained with 80% methanol as the extraction media. The highest values of total phenols and total flavonoids were found in the extract obtained with choline chloride-fructose NADES (36.15 ± 3.39 mg gallic acid g dry weight (DW) and 4.71 ± 0.33 mg rutin g DW, respectively). The extraction recoveries for the individual phenolic compounds depended strongly on the phenolic compound's structure, with relative mean values between 70% and 97%.