ABSTRACT The symbioses between corals and microorganisms, including the endosymbiotic dinoflagellates (family Symbiodiniaceae) and bacteria, are central to coral health and functioning. Certain species of Symbiodiniaceae in the genus Durusdinium are known to confer enhanced thermotolerance to corals and could therefore be beneficial under global climate change. However, association with thermotolerant algal symbionts may come with trade‐offs that affect long‐term coral persistence, and this study reports on one potentially consequential trade‐off. We exposed colonies of the coral Galaxea fascicularis hosting Symbiodiniaceae in the genus Cladocopium (C‐corals) or Durusdinium (D‐corals) to elevated temperature equivalent to ~9.5 degree heating weeks. While C‐corals were heat‐sensitive, as evidenced by reduced Symbiodiniaceae cell density, photochemical efficiency and tissue pigmentation, they were resilient to tissue loss, maintained a stable bacterial community under elevated temperature, and showed limited mortality (12.5%) at the end of the 15‐week recovery. Conversely, D‐corals showed limited Symbiodiniaceae photodamage or tissue pigmentation loss under elevated temperature and initially demonstrated heat resilience. However, D‐corals exhibited tissue loss and a significant reduction in newly formed polyps under elevated temperature, which occurred in parallel with a shift in their bacterial community composition toward taxa linked to bleaching, disease or algal overgrowth (e.g., Sphingomonas ). Most D‐corals died at the end of the recovery period. The intracellular bacterial communities in Cladocopium and Durusdinium freshly isolated from the experimental corals revealed symbiont‐specific patterns, where Durusdinium showed strong affiliation with the diazotroph Ruegeria sp. Our findings show that G. fascicularis associating with the thermally tolerant Durusdinium may have higher susceptibility to tissue loss relative to corals with Cladocopium symbionts. If this trade‐off occurs across corals that can associate with both Cladocopium and Durusdinium , it can have profound implications for reef persistence under global climate change, and further study is critical to inform conservation strategies aiming to build resilient reefs.