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Deforestation is the primary driver of carbon losses in tropical forests, but it does not operate alone. Forest fragmentation, a resulting feature of the deforestation process, promotes indirect carbon losses induced by edge effect. This process is not implicitly considered by policies for reducing carbon emissions in the tropics. Here, we used a remote sensing approach to estimate carbon losses driven by edge effect in Amazonia over the 2001 to 2015 period. We found that carbon losses associated with edge effect (947 Tg C) corresponded to one-third of losses from deforestation (2592 Tg C). Despite a notable negative trend of 7 Tg C year −1 in carbon losses from deforestation, the carbon losses from edge effect remained unchanged, with an average of 63 ± 8 Tg C year −1 . Carbon losses caused by edge effect is thus an additional unquantified flux that can counteract carbon emissions avoided by reducing deforestation, compromising the Paris Agreement’s bold targets.