Recent large scale carbon (C) emissions from deforestation have been estimated by combining remotely-sensed land use change information with satellite-based above ground biomass (AGB) data. However, these estimates are constrained to the satellite era while regions such as the Amazon Basin have been heavily impacted by deforestation before this period. Assessing the net contribution of past tropical deforestation to the growth in atmospheric CO2 is therefore challenging. We address this lack of data by constructing two maps of potential AGB with a machine learning algorithm trained on the relationship between AGB and climate and topography in intact forest landscapes of the Amazon Basin. Reconstructions converge to a current deficit of 11.5-12% in AGB, or a net loss of ~7-8 Pg C of AGB in the Amazon Basin compared to current estimates. This represents a net contribution of ~3.5 ppm of atmospheric CO2 or 3% of the historical growth.