Blackthorn (Prunus spinosa L.) is a wild, understudied plant rich in bioactive compounds such as polyphenols with designated antioxidant potential. The main objective of this research was to optimize ultrasound-assisted extraction of blackthorn pomace using natural deep eutectic solvents (NADES). To obtain the highest yield of polyphenols and improved in vitro antioxidant activity, response surface methodology (RSM) and central composite experimental design were used. The screening step of the study included ten different NADESs using a one-factor-at-a-time approach. Two NADES mixtures (N12, containing proline and lactic acid in a molar ratio of 1:2, and N14, containing choline chloride and glycerol in a molar ratio of 1:1) were chosen for the second step of the study, which aimed to select the most influential process parameters. A fractional factorial 2 design was used, varying five different parameters at two levels: extraction time (30 and 60 min), extraction temperature (40 and 50 °C), and liquid-to-solid ratio (10 and 20 mL/g), water content in NADES (15 and 20%), and NADES type (N12 and N14). After the second step, N12 containing 20% water was chosen as the most potent solvent for the optimization study. For the final step, the other three parameters were varied on three levels, and thus optimal conditions were obtained (extraction time 90 min, extraction temperature 65 °C, and liquid-to-solid ratio 22.65 mL/g). Blackthorn juice was also tested in the first step, as well as under optimal conditions established for pomace, in order to evaluate whether these conditions are suitable for juice and to determine the percentage of improvement in extraction efficiency.