Africa’s forests and woody savannas have historically acted as a carbon sink, removing atmospheric carbon and storing it as biomass. However, our novel analysis reveals a critical transition from a carbon sink to a carbon source between 2010 and 2017. Using new high-resolution satellite-derived biomass maps, validated with field plots and machine learning techniques, we quantified the aboveground biomass stocks across African biomes over a decade. Between 2007 and 2010, the continent gained 439 ± 66 Tg yr⁻1 of aboveground biomass, but from 2010 to 2015 biomass declined by − 132 ± 20 Tg yr-1 and from 2015 to 2017 this decline continued with a loss of − 41 ± 6 Tg yr-1, primarily driven by deforestation in tropical moist broadleaf forests. Gains in savanna biomass partially offset these losses, likely due to shrub encroachment. Our findings underline the urgent need for implementing policies to halt global deforestation as required by the Glasgow Leaders Declaration to close the global emissions gap. The current ongoing revisions of Nationally Determined Contributions to the Paris Agreement need to be even more ambitious to compensate for the ongoing loss of natural carbon sinks.