AbstractCarbon stocks and emissions are quantified using many different measures and metrics, and these differ in their surrogacy, measurement, and incentive value. To evaluate potential policy impacts of using different carbon measures, we modeled and mapped carbon in above-ground and below-ground stocks, as well as fluxes related to sequestration, oxidation and combustion in the Ex Mega Rice Project Area in Central Kalimantan, Indonesia. We identify significant financial and carbon emission mitigation consequences of proxy choice in relation to the achievement of national emissions reduction targets. We find that measures of above-ground biomass carbon stock have both high measurement and incentive value, but low surrogacy for potential emissions or the potential for emissions reductions. The inclusion of below-ground carbon increased stocks and flows by an order of magnitude, highlighting the importance of protecting and managing soil carbon and peat. Carbon loss and potential emissions reduction is highest in the areas of deep peat, which supports the use of deep peat as a legislative metric. Divergence in patterns across sub-regions and through time further emphasizes the importance of proxy choice and highlights the need to carefully consider the objectives of the application to which the measure of carbon will be applied.