Fishes faced with novel thermal conditions often modify physiological functioning to compensate for elevated temperatures. This physiological plasticity (thermal acclimation) has been shown to improve metabolic performance and extend thermal limits in many species. Adjustments in cardiorespiratory function are often invoked as mechanisms underlying thermal plasticity because limitations in oxygen supply have been predicted to define thermal optima in fishes, however few studies have explicitly linked cardiorespiratory plasticity to metabolic compensation. Here we quantify thermal acclimation capacity in the commercially harvested Nile perch (Lates niloticus) of East Africa, and investigate mechanisms underlying observed changes. We reared juvenile Nile perch for 3 months under two temperature regimes, and then measured a series of metabolic traits (e.g., aerobic scope, AS) and critical thermal maximum (CTmax) upon acute exposure to a range of experimental temperatures. We also measured morphological traits of heart ventricles, gills, and brains to identify potential mechanisms for compensation. We found that long-term (3-months) exposure to elevated temperature induced compensation in upper thermal tolerance (CTmax) and metabolic performance (SMR, MMR and AS), and induced cardiac remodeling in Nile perch. Furthermore, variation in heart morphology influenced variations in metabolic function and thermal tolerance. These results indicate that plastic changes enacted over longer exposures lead to differences in metabolic flexibility when acutely exposed to temperature variation. Furthermore, we established functional links between cardiac plasticity, metabolic performance, and thermal tolerance, providing evidence that plasticity in cardiac capacity may be one mechanism for coping with climate change.