To investigate plasticity in biochemical and physiological health attributes of corals, identical colony fragments of the coral Acropora tenuis, from two inshore populations, were exposed to native and novel environmental regimes. Variation in global gene expression (GE) and lipid and fatty acid (FA) composition of surviving fragments of experimental colonies was quantified after four months. This study demonstrates the strong influence of a source effect defining gene expression relating to basic biological functions, including biosynthetic processing, translation and ribosome biogenesis. However, there is plasticity in specific genes relating to elevated health and immunity, which can respond to changes in environmental conditions. These findings suggest hope for future corals, if we can reduce anthropogenic water quality stressors.