Coral reefs are suffering unprecedented declines in health state on a global scale. Some have suggested that human assisted evolution or assisted gene flow may now be necessary to effectively restore reefs and pre-condition them for future climate change. An understanding of the key metabolic processes in corals, including under stressed conditions, would greatly facilitate the effective application of such interventions. To date, however, there has been little research on corals at this level, particularly regarding studies of the metabolome of Scleractinian corals. Here, the metabolomic profiles [measured using 1H nuclear magnetic resonance spectroscopy (1H NMR) and ultra-high-performance liquid chromatography-mass spectrometry (LC-MS)] of two dominant reef building corals, Acropora hyacinthus and A. millepora, from two distinct geographical locations (Australia and Singapore) were characterized. We assessed how an acute temperature stress (an increase of 3.25°C ± 0.28 from ambient control levels over 8 days), shifted the corals’ baseline metabolomic profiles. Regardless of the profiling method utilized, metabolomic signatures of coral colonies were significantly distinct between coral species, a result supporting previous work. However, this strong species-specific metabolomic signature appeared to mask any changes resulting from the acute heat stress. On closer examination, we were able to discriminate between control and temperature stressed groups using a partial least squares discriminant analysis classification model (PLSDA). However, in all cases “late” components needed to be selected (i.e., 7 and 8 instead of 1 and 2), suggesting any treatment effect was small, relative to other sources of variation. This highlights the importance of pre-characterizing the coral colony metabolomes, and of factoring that knowledge into any experimental design that seeks to understand the apparently subtle metabolic effects of acute heat stress on adult corals. Further research is therefore needed to decouple these apparent individual and species-level metabolomic responses to climate change in corals.