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An organism's size, known to affect biological structures and processes from cellular metabolism to population dynamics, depends upon the duration and rate of growth. However, it is still poorly understood how mitochondrial function affects the energetic basis of growth, especially in ectotherms, which represent a huge majority of animal biodiversity. Here, we present an intraspecies comparison of neighboring populations of frogs (Rana temporaria) that have large differences in body mass even at the same age. By investigating liver mitochondrial bioenergetics, we find that frogs with high growth rates and large body sizes exhibit higher ATP synthesis rates and more efficient oxidative phosphorylation compared to the smaller frogs with low growth rates. This higher energy transduction efficiency is not associated with significant increased oxidative capacity or membrane potential values, but instead may rely on a higher mitochondrial phosphorylation system activity in combination with a lower inner membrane proton leakage. Overall, the present study introduces the mitochondrial energy transduction system as an important mechanism for balancing physiological and ecological trade-offs associated with body size. Whether phenotype differences in mitochondrial function result from local ecological constraints or reflect a natural genetic variability within wild populations of common frogs remains an open question. However, our findings highlight the need for closer consideration of all aspects of mitochondrial metabolism for a better understanding of the physiological basis of the link between size, metabolism, and energy production in wild-dwelling organisms.