It is widely acknowledged that temperature stress affects an organism’s sensitivity to ocean acidification and vice versa, yet it is not clear how the two are mechanistically linked. Here, we induced thermal stress in two coral species with differing bleaching susceptibilities to measure how a reduction in photosynthetic performance impacts intracellular pH (pHi) regulation in the symbiotic dinoflagellates (Symbiodinium sp.) and their host coral cells. Our hypothesis was that thermally induced photosynthetic dysfunction in the symbiont would prevent the efficient removal of additional CO2, lowering its buffering capacity and thus increasing the host cell’s susceptibility to intracellular acidosis. To test this, we exposed Pocillopora damicornis (a thermally sensitive coral) and Montipora capitata (a thermally resilient coral) to four different temperature treatments (23.8, 25.5, 28 and 31 °C) for 1 week. We then isolated intact symbiotic coral endodermal cells, placed them in a live-cell chamber attached to a confocal microscope and bathed them in CO2-acidified seawater (~pH 7.6) for 30 min, before measuring the light-adapted pHi of both the host cell and its symbiont. Cells isolated from P. damicornis were more prone to cellular acidosis (declines in pHi of 11 and 8 % in host and symbiont, respectively, at 31 °C relative to 23.8 °C) than cells isolated from M. capitata (5 and 4 %, respectively). These results highlight the important role of Symbiodinium productivity (in addition to a range of physico-chemical factors such as skeletal morphology and tissue pigmentation) in determining the sensitivity of corals to rising sea surface temperatures and ocean acidification.