Probiotic inoculation is one of several interventions currently being developed with the aim of increasing climate resilience in corals. Inspired by the oxidative stress theory of coral bleaching, we investigated whether a probiotic comprised of bacteria isolated from the coral model, Exaiptasia diaphana, and designed to scavenge free radicals could improve thermal tolerance of this anemone. We tested our probiotic alongside low free radical scavenging and no-inoculum control treatments under ambient and elevated temperature conditions but found no evidence for improved thermal tolerance. Changes in the relative abundance of anemone-associated Labrenzia provided strong evidence for probiotic integration in the E. diaphana microbiome. Uptake of other probiotic members was inconsistent and probiotic members did not persist in the anemone microbiome over time. Consequently, the failure of probiotic inoculation to confer improved thermal tolerance may have been due to the absence of probiotic bacteria for the full duration the experiment. Importantly, there were no apparent physiological impacts on the holobiont following inoculation, thus showing that shifting the abundance of naturally occurring anemone microbiome members is not detrimental. Given the frequency of coral bleaching events, without urgent intervention to achieve coral resilience to climate change, coral reefs will not survive. This study will therefore be invaluable for future bacterial bioengineering approaches.