Maqui (Aristotelia chilensis (Mol.) Stuntz) is a Chilean berry rich in antioxidants, which are mostly found in the pulp and skin of the fruit. The objective was to evaluate the cryoconcentration process by centrifugation–filtration as a simultaneous, efficient, and innovative method to increase the content of thermosensitive bioactive compounds of aqueous maqui extract. Cryoconcentration separated the concentrated solute from the aqueous maqui extract with an efficiency of more than 95%; it increased the content of total polyphenols and total anthocyanins and antioxidant capacity by 280%, 573%, and 226%, respectively. Although the concentrates obtained by evaporation at 50, 70, and 80 °C increased the content of bioactive compounds, they did so in a lower percentage than the cryoconcentrate. Furthermore, cyanidin 3,5-diglucoside was degraded at 70 and 80 °C. In conclusion, cryoconcentration by centrifugation–filtration as a simultaneous process efficiently separates the solutes from the frozen matrix of aqueous maqui extract, and it maintains and increases the contents of polyphenols and anthocyanins and antioxidant capacity. This method is recommended for concentrating natural berry extracts with thermosensitive compounds.