Human-induced ocean acidification and warming alter seawater carbonate chemistry reducing the calcification of reef-building crustose coralline algae (CCA), which has implications for reef stability. However, due to the presence of multiple carbonate minerals with different solubilities in seawater, the algal mineralogical responses to changes in carbonate chemistry are poorly understood. Here we demonstrate a 200% increase in dolomite concentration in living CCA under greenhouse conditions of high pCO2 (1,225 μatm) and warming (30 °C). Aragonite, in contrast, increases with lower pCO2 (296 μatm) and low temperature (28 °C). Mineral changes in the surface pigmented skeleton are minor and dolomite and aragonite formation largely occurs in the white crust beneath. Dissolution of high-Mg-calcite and particularly the erosive activities of endolithic algae living inside skeletons play key roles in concentrating dolomite in greenhouse treatments. As oceans acidify and warm in the future, the relative abundance of dolomite in CCA will increase.