Elevated CO₂ levels have been shown to affect metabolic performance in some coral reef fishes. However, all studies to date have employed stable elevated CO₂ levels, whereas reef habitats can experience substantial diel fluctuations in pCO₂ ranging from ±50 to 600 μatm around the mean, fluctuations that are predicted to increase in magnitude by the end of the century. Additionally, past studies have often investigated the effect of elevated CO₂ in isolation, despite the fact that ocean temperatures will increase in tandem with CO₂ levels. Here, we tested the effects of stable (1000 μatm) versus diel-cycling (1000 ± 500 μatm) elevated CO₂ conditions and elevated temperature (+2 °C) on metabolic traits of juvenile spiny damselfish, Acanthochromis polyacanthus. Resting oxygen uptake rates (ṀO₂) were higher in fish exposed to stable elevated CO₂ conditions when compared to fish from stable control conditions, but were restored to control levels under diel CO₂ fluctuations. However, the benefits of diel CO₂ fluctuations were diminished at elevated temperature. Factorial aerobic scope showed a similar pattern, but neither maximal ṀO₂ nor absolute aerobic scope was affected by CO₂ or temperature. Our results suggest that diel CO₂ cycles can ameliorate the increased metabolic cost associated with elevated CO₂, but elevated temperature diminishes the benefits of diel CO₂ cycles. Thus, previous studies may have misestimated the effect of ocean acidification on the metabolic performance of reef fishes by not accounting for environmental CO₂ fluctuations. Our findings provide novel insights into the interacting effects of diel CO₂ fluctuations and temperature on the metabolic performance of reef fishes.