We investigated the impacts of carbon dioxide (CO2)-induced acidification on energy metabolism in muscle tissue of rainbow trout Oncorhynchus mykiss fry. Fry were exposed to freshwater in equilibrium with air containing CO2 at volume concentrations of 380, 1000 and 2000 ppm for 30 days. At this critical and sensitive life stage, we showed dose-dependent reductions in weight gain and changes in energy metabolism under projected future CO2 levels. Rainbow trout fry exposed to elevated CO2 concentrations produced more energy in muscle tissue because ATP levels were significantly elevated. Fry exposed to 1000 ppm CO2 had a higher activity of pyruvate kinase (PK), higher concentrations of pyruvate, acetate, 2-oxoglutarate, phenylalanine, tyrosine, inosine, uracil and uridine, and lower concentrations of anserine and IMP in muscle tissue based on metabolomic analysis. We infer that the increased ATP production in fry exposed to 1000 ppm CO2 is produced through glycolysis. In the 2000 ppm group, the protein content of muscle was lower than in the control, and the activities of PK, cytochrome C oxidase (COX), Na+/K+-ATP and Ca2+/Mg2+-ATPase were significantly higher. Concentrations of pyruvate, 2-oxoglutarate, histidine, anserine and IMP were significantly lower, and alanine, methionine, leucine, isoleucine, valine, lysine, pantothenate, uracil and inosine were significantly higher. Accelerated tissue decomposition may have sustained the higher production of ATP in the 2000 ppm group.