Giant clams produce massive calcified shells with important biological (e.g., defensive) and ecological (e.g., habitat-forming) properties. Whereas elevated seawater temperature is known to alter giant clam shell structure, no study has examined the effects of a simultaneous increase in seawater temperature and partial pressure of carbon dioxide (pCO2) on shell mineralogical composition in these species. We investigated the effects of 60-days exposure to end-of-the-century projections for seawater temperature (+ 3 °C) and pCO2 (+ 500 µatm) on growth, mineralogy, and organic content of shells and scutes in juvenile Tridacna squamosa giant clams. Elevated temperature had no effect on growth rates or organic content, but did increase shell [24Mg]/[40Ca] as well as [40Ca] in newly-formed scutes. Elevated pCO2 increased shell growth and whole animal mass gain. In addition, we report the first evidence of an effect of elevated pCO2 on element/Ca ratios in giant clam shells, with significantly increased [137Ba]/[40Ca] in newly-formed shells. Simultaneous exposure to both drivers greatly increased inter-individual variation in mineral concentrations and resulted in reduced shell N-content which may signal the onset of physiological stress. Overall, our results indicate a greater influence of pCO2 on shell mineralogy in giant clams than previously recognized.