Ocean warming and acidification are threatening marine ecosystems. In marine animals, acidification is thought to enhance ion regulatory costs and thereby baseline energy demand, while elevated temperature also increases baseline metabolic rate. Here we investigated standard metabolic rates (SMR) and plasma parameters of Atlantic cod (Gadus morhua) after 3–4 weeks of exposure to ambient and future PCO<inf>2</inf> levels (550, 1200 and 2200 µatm) and at two temperatures (10, 18 °C). In vivo branchial ion regulatory costs were studied in isolated, perfused gill preparations. Animals reared at 18 °C responded to increasing CO<inf>2</inf> by elevating SMR, in contrast to specimens at 10 °C. Isolated gills at 10 °C and elevated PCO<inf>2</inf> (≥1200 µatm) displayed increased soft tissue mass, in parallel to increased gill oxygen demand, indicating an increased fraction of gill in whole animal energy budget. Altered gill size was not found at 18 °C, where a shift in the use of ion regulation mechanisms occurred towards enhanced Na⁺/H⁺-exchange and HCO<inf>3</inf> ⁻ transport at high PCO<inf>2</inf> (2200 µatm), paralleled by higher Na⁺/K⁺-ATPase activities. This shift did not affect total gill energy consumption leaving whole animal energy budget unaffected. Higher Na⁺/K⁺-ATPase activities in the warmth might have compensated for enhanced branchial permeability and led to reduced plasma Na⁺ and/or Cl⁻ concentrations and slightly lowered osmolalities seen at 18 °C and 550 or 2200 µatm PCO<inf>2</inf> in vivo. Overall, the gill as a key ion regulation organ seems to be highly effective in supporting the resilience of cod to effects of ocean warming and acidification.