This study assessed the energy budget for juvenile Atlantic Sea Scallop, Placopecten magellanicus, during a natural drop in temperature (15.6°C to 5.8°C) over an 8-week time period during the fall at three different enrichment levels of carbon dioxide (CO2). Every 2 weeks, individuals were sampled for ecophysiological measurements of feeding activity, respiration rate (RR) and excretion rate (ER) to enable the calculation of scope for growth (SFG) and atomic oxygen:nitrogen ratios (O:N). In addition, 36 individuals per treatment were removed for shell height, dry tissue weight (DTW) and dry shell weight (DSW). We found a significant decrease in feeding rates as CO2 increased. Those rates also were significantly affected by temperature, with highest feeding at 9.4°C. No significant CO2 effect was observed for catabolic energy processes (RR and ER); however, these rates did increase significantly with temperature. The O:N ratio was not significantly affected by CO2, but was significantly affected by temperature. There was a significant interaction between CO2 and temperature for ER and the O:N ratio, with low CO2 levels resulting in a U-shaped response that was not sustained as CO2 levels increased. This suggests that the independent effects of CO2 and temperature observed at low levels are different once a CO2 threshold is reached. Additionally, there were significant differences in growth estimators (shell height and DSW), with the best growth occurring at the lowest CO2 level. In contrast to temperature variations that induced a trade-off response in energy acquisition and expenditure, results from this research support the hypothesis that sea scallops have a limited ability to alter physiological processes to compensate for increasing CO2.