The carbon isotope 13C is commonly used to attribute the last deglacial atmospheric CO2 rise to various processes. Here we show that the growth of the world's largest reef system, the Great Barrier Reef (GBR), is marked by a pronounced decrease in δ13C in absolutely dated fossil coral skeletons between 12.8 and 11.7 ka, which coincides with a prominent minimum in atmospheric δ13CO2 and the Younger Dryas. The event follows the flooding of a large shelf platform and initiation of an extensive barrier reef system at 13 ka. Carbon cycle simulations show the coral δ13C decrease was mainly caused by the combination of isotopic fractionation during reef carbonate production and the decomposition of organic land carbon on the newly flooded shallow-water platform. The impacts of these processes on atmospheric CO2 and δ13CO2, however, are marginal. Thus, the GBR was not contributing to the last deglacial δ13CO2 minimum at ∼12.4 ka.