Carbonate rocks on continental crust are one of Earth’s largest reservoirs of CO2 and yet the controls on their volume through time are poorly understood. Here we quantify temporal changes in preserved continental carbonate rocks over the last billion years in both global and North America-specific datasets within paleogeographic context. We find the preserved area of continental carbonate rocks increases by ~175% across the Neoproterozoic-Phanerozoic boundary ca. 539 million years ago, coincident with the rise of macroscopic, multicellular life and the evolutionary innovation of carbonate biomineralization in shallow water reefs. We demonstrate that crustal loading from carbonate sediments on one tropical paleo-continent (North America) contributes to an increase in continent-scale accommodation in the early Phanerozoic, expanding shallow marine environments. We predict this feedback between enhanced carbonate accumulation and subsidence was an important component of the termination of the Great Unconformity. These results are combined into a new conceptual model that links the changes in preserved carbonate rock volumes to the evolutionary innovation of carbonate biomineralization in a range of complex organisms. Our model implies evolutionary controls on the carbonate rock reservoir enhanced CO2 sequestration at the beginning of the Phanerozoic, with consequences for Earth’s carbon cycle, climate and habitability.