Metabolism constitutes a fundamental property of all organisms. Metabolic rate is commonly described to scale as a power function of body size and exponentially with temperature, thereby treating the effects of body size and temperature independently. Mounting evidence shows that the scaling of metabolic rate with body mass itself depends on temperature. Across-species analyses in fishes suggest that the mass-scaling exponent decreases with increasing temperature. However, whether this relationship holds at the within-species level has rarely been tested. Here, we re-analyse data on the metabolic rates of four freshwater fish species, two coregonids and two cyprinids, that cover wide ranges of body masses and their naturally experienced temperatures. We show that the standard metabolic rate of the coregonids is best fit when accounting for a linear temperature dependence of the scaling of metabolic rate with body mass, whereas a constant mass-scaling exponent is supported in case of the cyprinids. Our study shows that phenotypic responses to temperature can result in temperature-dependent scaling relationships at the species level and that these responses differ between taxa. Together with previous findings, these results indicate that evolutionarily adaptive and phenotypically plastic responses to temperature affect the scaling of metabolic rate with body mass in fishes.