Exposure to future ocean acidification scenarios may alter the behaviour of marine teleosts through interference with neuroreceptor functioning. So far, most studies investigated effects of ocean acidification on the behaviour of fish, either isolated or in combination with environmental temperature. However, only few physiological studies on this issue were conducted despite the putative neurophysiological origin of the CO2-induced behavioural changes. Here, we present the metabolic consequences of long-term exposure to projected ocean acidification (396–548 μatm PCO2 under control and 915–1272 μatm under treatment conditions) and parallel warming in the brain of two related fish species, polar cod (Boreogadus saida, exposed to 0 °C, 3 °C, 6 °C and 8 °C) and Atlantic cod (Gadus morhua, exposed to 3 °C, 8 °C, 12 °C and 16 °C). It has been shown that B. saida is behaviourally vulnerable to future ocean acidification scenarios, while G. morhua demonstrates behavioural resilience.