A prominent goal of policies mitigating climate change and biodiversity loss is to achieve zero deforestation in the global supply chain of key commodities, such as palm oil and soybean. However, the extent and dynamics of deforestation driven by commodity expansion are largely unknown. Here we mapped annual soybean expansion in South America between 2000 and 2019 by combining satellite observations and sample field data. From 2000 to 2019, the area cultivated with soybean more than doubled from 26.4 Mha to 55.1 Mha. Most soybean expansion occurred on pastures originally converted from natural vegetation for cattle production. The most rapid expansion occurred in the Brazilian Amazon, where soybean area increased more than tenfold, from 0.4 Mha to 4.6 Mha. Across the continent, 9% of forest loss was converted to soybean by 2016. Soybean-driven deforestation was concentrated at the active frontiers, nearly half located in the Brazilian Cerrado. Efforts to limit future deforestation must consider how soybean expansion may drive deforestation indirectly by displacing pasture or other land uses. Holistic approaches that track land use across all commodities coupled with vegetation monitoring are required to maintain critical ecosystem services.