Benthic habitats such as intertidal areas, sandy or rocky shores, upwelling zones, and estuaries are characterized by variable environmental conditions. This high variability of environmental stressors such as temperature, salinity, and pH/pCO2 levels have been shown to impose restrictions on organismal performance. The giant mussel Choromytilus chorus forms intertidal and subtidal mussel beds in estuarine zones associated with fjords occurring in southern Chile and is an important aquacultural resource in Patagonia. In this study, we estimated the sensitivity of physiological traits and energy balance of C. chorus juveniles exposed to 3 pCO2 treatments (500, 750, and 1200 µatm) for 30 d. Results showed that in acidified, high pCO2 conditions, C. chorus juveniles had increased metabolic rates; however, other physiological traits (clearance and ingestion rates, ammonia excretion, absorption efficiency, growth rate, biomass production, net calcification, and dissolution rates) were not affected. These results suggest that when subjected to acidification, the adaptive response of C. chorus triggers tradeoffs among physiological traits that favor sustained feeding and growth in order to combat increased metabolic stress. As has been reported for other marine organisms, chronic exposure to variable pH/pCO2 in their native habitats, such as estuarine zones, could explain the differential acclimatization capacity of giant mussels to cope with the increase in pCO2. Additionally, the fact that the mussels did not suffer from mortality indicates that increased pCO2 levels may have chronic, but not lethal, effects on this species under these experimental conditions.