Mixotrophic organisms can derive nutrition from both auto- and heterotrophy, which allows them to use a variety of trophic pathways to sustain their metabolic demands under variable conditions. Therefore, when facing environmental change, these organisms are expected to demonstrate an intrinsic ability to acclimatize through trophic plasticity. Scleractinian corals are ecologically important mixotrophs, but understanding their trophic plasticity has been impaired by an oversimplification towards inconsistent proxies of coral diet and overlooking intraspecific variability. Here, we applied a Bayesian analysis of carbon and nitrogen stable isotope data to determine the trophic niches of six common species of scleractinian corals and their associated endosymbionts, and combined it with an unsupervised machine learning algorithm to identify trophic behaviours and strategies. We found a variable amount of nutritional plasticity identified by different trophic behaviours within and between mixotrophic corals living under the same environmental conditions. Furthermore, we observed changes in trophic plasticity across environmental conditions. Corals from variable environments had larger host and endosymbiont niches than corals from stable environments. In addition, deeper corals had niches indicating a greater degree of heterotrophy than shallow corals. Collectively, corals exhibited distinct trophic strategies by promoting trophic niche differentiation along the mixotrophic continuum and conspecific individual colonies displayed high trophic variation. Our results provide a foundation to understand how mixotrophic organisms may adjust their nutrition in response to ongoing global environmental change and the consequential modification of benthic assemblages.