Migration of corals through a hot water bottleneck in the Southern Red Sea, following the last glacial period, has led to a situation where corals in the Northern Red Sea now express high thermal thresholds while living at suboptimal lower temperatures. We tested to what extent the coral Stylophora pistillata is capable of resisting future ocean conditions as a result of this selection. We combined chlorophyll fluorescence analysis, biochemical markers, and respirometry with state of the art correlative TEM and NanoSIMS techniques to obtain a holistic picture on the physiological impact of the isolated and combined effects of temperature (+5°C) and pH (-0.3 units relative to ambient). After 2 months, most physiological variables were either unaffected or improved by the combined effect of high temperature and low pH. Net oxygen production effectively doubled due to changes in photochemistry and higher symbiont pigmentation, and we observed higher values for holobiont productivity with P:R ratios of up to 1.72. No significant change in the activity of enzymatic antioxidants or daily calcification was detected. NanoSIMS data revealed that carbon and nitrogen assimilation in the symbiont and host gastrodermis are negatively affected by isolated temperature stress. However, no difference in the proportion of symbiont-derived carbon in the host lipids was observed and neither protein nor overall carbohydrate content was affected in either partner. Our data point to a high degree of physiological resistance of this coral to the expected global trends in ocean conditions and emphasize the urgency of reducing local stressors in this region.