After more than five centuries of land exploitation, Brazil has lost more than one-third of its natural vegetation. Changes in land use and land cover (LULC) are destabilizing soil organic carbon (SOC) stocks and increasing greenhouse gas (GHG) emissions. Current estimates put Brazil’s SOC stocks at 37 petagrams (Pg) in the top 30 cm of soil. However, the total amount of SOC lost since 1500 is unknown. We hypothesize that Brazil has lost at least one-third of its SOC since 1500, particularly in the Atlantic Forest. This biome, characterized by environmental conditions ideal for organic soil formation, has experienced extensive deforestation and land-use change. We will integrate current and historical land-use data, artificial intelligence, and expert knowledge to test this hypothesis to reconstruct historical SOC stocks. This information has important implications for greenhouse gas accounting, climate policy, and the carbon credit market.