The use of coral probiotics, i.e. beneficial microorganisms for corals (BMCs), is a novel approach to enhancing coral health under heat stress. While BMCs mitigate coral bleaching and mortality during prolonged heat stress conditions, their effectiveness in mitigating short-term acute heat stress remains understudied. This study investigates the effects of BMCs on two Red Sea hard coral species, Acropora cf. hemprichii and Pocillopora verrucosa, during short-term heat stress. Twelve coral fragments per species were allocated to each treatment across two temperature regimes (26◦C and 32◦C) for 48 hours, with half receiving BMC inoculation and half serving as controls. Results show BMC supplementation significantly prevented mortality in Acropora cf. hemprichii at 32◦C, contrasting with a 100% mortality observed in the control group. Specifically, probiotic-inoculated Acropora cf. hemprichii at 32◦C exhibited preserved primary production, a 12–13 fold increase in algal cell densities, 4–5 times higher FV/Fm ratios, and 4–5 and 2–3 times higher chlorophyll a and c2 concentrations, respectively, compared to their untreated conspecifics. All P. verrucosa colonies survived the 32◦C exposure without tissue loss or reduced holobiont function in both control and BMC treatments. These findings underscore the rapid effects of BMC inoculation, initiated just 2 hours prior to acute heat stress, in protecting heat-sensitive Acropora cf. hemprichii against mortality and adverse photo-physiological changes, with beneficial effects visible within 2 days. Recognizing the critical timeframe for beneficial effects is paramount for management strategies to address heat-sensitive corals on natural reefs, such as implementing probiotic interventions before anticipated marine heatwaves.