Fertile soil known as Amazonian dark earth is central to the debate over the size and ecological impact of ancient human populations in the Amazon. Dark earth is typically associated with human occupation, but it is uncertain whether it was created intentionally. Dark earth may also be a substantial carbon sink, but its spatial extent and carbon inventory are unknown. We demonstrate spatial and compositional similarities between ancient and modern dark earth and document modern Indigenous practices that enrich soil, which we use to propose a model for the formation of ancient dark earth. This comparison suggests that ancient Amazonians managed soil to improve fertility and increase crop productivity. These practices also sequestered and stored carbon in the soil for centuries, and we show that some ancient sites contain as much carbon as the above-ground rainforest biomass. Our results demonstrate the intentional creation of dark earth and highlight the value of Indigenous knowledge for sustainable rainforest management.