Previous studies suggest uniform reductions in coral calcification under ocean acidification (OA); however, greater tolerance has been observed under natural diel metabolic signals present on reefs. In addition, few studies have examined the role of in hospite zooxanthellae energetics on coral OA tolerance. In this study, we examined zooxanthellae photosynthesis and coral calcification responses using seawater with natural metabolic dissolved inorganic carbon (DIC) dynamics from a fringing back reef on Little Cayman Island, Caribbean. The experimental design included Acropora cervicornis and Porites divaricata microcolonies grown in continuously flowing seawater with (∼1000 μatm) and without (∼500 μatm) CO2 enrichment to year 2100 predicted levels. Calcification rates were measured weekly, while linear extension and zooxanthellae photosynthesis were determined at the termination of the 28 d experiment. Results showed A. cervicornis microcolonies maintained both photosynthesis and calcification under elevated CO2 partial pressure (pCO2) relative to controls. However, photosynthesis and calcification rates of P. divaricata microcolonies were reduced by ∼80 and 20%, respectively, under relatively high [DIC]:[H+] ratios and aragonite saturation states (Ωarag). Porites divaricata calcification response to elevated pCO2 was linked to photophysiological dysfunction of the algal symbiont, an indicator that this species was metabolically depressed under elevated pCO2. In contrast to calcification, linear extension rates were unaffected by pCO2 in both species. Future studies should investigate how elevated pCO2 may compromise zooxanthellae–coral interactions with an emphasis on DIC uptake pathways.