Bleaching events in the marine environment are now occurring globally, and the frequency and severity of these events are increasing. Here we investigate the impact of thermal stress exposure, both ex situ and in situ, on the meta-organism responses of the scleractinian coral species Pocillopora damicornis. Using mesocosms to recreate warming scenarios previously observed at Heron Island, we show that P. damicornis symbiont densities and photophysiological parameters decline at a similar rate under thermal stress regardless of warming scenario. However, we find that the P. damicornismicrobiome remains stable over time regardless of thermal stress. Our study therefore suggests that while P. damicornis is physiologically impacted by bleaching temperatures, the microbial community remains unchanged. Given that P. damicornis is a common environmental generalist in the Indo-Pacific, we further explore if the observed microbial stability is characteristic of P. damicornis during in situ bleaching events at Heron Island and Lord Howe Island, two geographically distinct locations with different bleaching temperature thresholds. The widespread distribution of environmental generalist coral species suggests their potential contribution to coral reef structure under future climate conditions, and the link between environmental conditions and the bleaching responses of the coral meta-organism needs to be determined.