Research interest regarding maqui (Aristotelia chilensis) has increased over the last years due to its potential health benefits as one of the most antioxidant-rich berries. Ultrasound-assisted extraction (UAE) is an advanced green, fast, and ecological extraction technique for the production of high quality extracts from natural products, so it has been proposed in this work as an ideal alternative extraction technique for obtaining extracts of high bioactivity from maqui berries. In order to determine the optimal conditions, the extraction variables (percentage of methanol, pH, temperature, ratio “sample mass/volume of solvent”, amplitude, and cycle) were analyzed by a Box-Behnken design, in conjunction with the response surface method. The statistical analysis revealed that the temperature and the percentage of methanol were the most influential variables on the extraction of the total phenolic compounds and total anthocyanins, respectively. The optimal extraction time was determined at 15 min for total phenolic compounds, while it was only 5 min for anthocyanins. The developed methods showed a high precision level with a coefficient of variation of less than 5%. Finally, the new methods were successfully applied to several real samples. Subsequently, the results were compared to those that were obtained in previous experiments by means of microwave assisted extraction (MAE). Similar extraction yields were obtained for phenolic compounds under optimized conditions. However, UAE proved to be slightly more efficient than MAE in the extraction of anthocyanins.