Mitochondrial respiration is a multi-step pathway that involves matrix and membrane-associated enzymes and plays a key role in acclimation to variable environmental conditions, but until now it has not been clear which of these steps would be most important in acclimation to changing temperatures and CO2 levels. Considering scenarios of ocean warming and acidification we assessed the role and limitation to phenotypic plasticity in the hearts of two Gadoid species adapted to different thermal ranges: the polar cod (Boreogadus saida), an Arctic stenotherm, and the Northeast Arctic population of Atlantic cod (NEAC, Gadus morhua), a cold eurytherm. We analysed the capacity of single enzymes involved in mitochondrial respiration [citrate synthase (CS), succinate dehydrogenase (SDH), cytochrome c oxidase (CCO)], the capacity of the electron transport system and the lipid class composition of the cellular membranes. Juveniles of the two species were held for four months at four temperatures (0, 3, 6, 8 °C for polar cod and 3, 8, 12, 16 °C for NEAC), at both ambient and elevated PCO2 (400 µatm and 1170 µatm, respectively). Polar cod showed no changes in mitochondrial enzyme capacities and in the relative lipid class composition in response to altered temperature or elevated PCO2. The lack of cardiac cellular plasticity together with evidence at the whole-animal level coming from other studies is indicative of little or no ability to overcome stenothermy, in particular during acclimation to 8 °C. In contrast, eurythermal NEAC exhibited modifications of membrane composition towards a more rigid structure and altered enzyme capacities to preserve functionality at higher temperatures. Furthermore, in NEAC, the capacities of SDH, CCO and CS were increased by high levels of CO2 if combined with high temperatures (12 and 16 °C), suggesting the compensation of an inhibitory effect. These results indicate that the cold eurythermal species (NEAC) is able to alter its mitochondrial function to a far greater extent than the Arctic stenotherm (polar cod), indicating greater resilience to variable environmental conditions. This difference in plasticity may underpin differences in the resilience to climate change and affect future species distributions and, eventually, survival.