Coral populations from reef habitats that experience extreme daily abiotic fluctuations have been suggested as candidates to survive and proliferate under future climate change. Few studies, however, have exposed corals from dynamic environments to the synergistic effects of ocean warming and acidification to investigate whether tolerance of present‐day environmental variability is maintained under future climate stress. This study assessed the impact of RCP2.6 (+0.8°C and +25 ppm) and RCP4.5 (+1.3°C and +66 ppm) ocean warming and acidification on the survivorship, primary calcification (i.e., extension), secondary calcification (i.e., densification), and protein densities of Isopora palifera originating from two distinct reef habitats (abiotically variable reef flat vs. stable reef slope) over 9 weeks. Temperature and pCO2 were offset from a reef slope baseline temperature of 26.0°C ± 0.6°C and pCO2 concentration of 559 ± 56 ppm, incorporating natural diurnal variability. A trade‐off was observed in I. palifera originating from the reef flat, which significantly increased tissue protein densities but reduced densification relative to corals from the reef slope. Survivorship nor extension rates differed between corals originating from the variable or stable reef habitats. Mortality increased under RCP4.5 as extension rates increased, indicating that energetic investment in skeletal expansion becomes unsustainable under future climate stress. Increasing temperature and CO2 reduced calcification rates irrespective of the corals originating reef habitat suggesting with future climate change, exposure to greater environmental variability may not benefit coral calcification. These results demonstrate that tolerance to present‐day abiotic variability does not necessarily infer resilience to moderate future ocean warming and acidification conditions.