Among the theories conceived to explain the natural world using a few and relatively simple assumptions and parameters, the Metabolic Theory of Ecology (MTE) stands out. It assumes metabolism as the biological pacemaker of processes from molecular to evolutionary scales. The MTE basically uses the old, well-known allometric scaling relations among metabolism, organism mass and temperature to explain the structure and function of cells, individuals, populations, communities and ecosystems. Although some predictions made by the MTE are remarkably accurate, especially for simple processes and when broad ranges of individual biomass and temperature are considered, like any general model the MTE sacrifices precision and thus realism to achieve its generality. MTE has logical inconsistencies and unexplained discrepancies with empirical data that are especially important regarding pelagic marine ecosystems in high latitudes. Interspecific and intraspecific differences in the responses of zooplankton metabolic processes to identical temperature and individual-mass changes, differences not accounted for by the MTE, could result in crucial deviations in ecosystem energy balance and biogeochemical cycles, implying low predictive value. The objective of this paper is to draw attention to the applicability and limits of the MTE as a predictive tool, especially for complex, second-order ecological processes.