There is growing recognition of the potential of large-scale forest restoration in the Amazon as a “nature-based solution” to climate change. However, our knowledge of forest loss and recovery beyond Brazil is limited, and carbon emissions and accumulation have not been estimated for the whole biome. Combining a 33-year land cover dataset with estimates of above-ground biomass and carbon sequestration rates, we evaluate forest loss and recovery across nine Amazonian countries and at a local scale. We also estimate the role of secondary forests in offsetting old-growth deforestation emissions and explore the temporal trends in forest loss and recovery. We find secondary forests across the biome to have offset just 9.7% of carbon emissions from old-growth deforestation, despite occupying 27.6% of deforested land. However, these numbers varied between countries ranging from 9.0% in Brazil to 23.8% in Guyana for carbon offsetting, and 24.8% in Brazil to 56.9% in Ecuador for forest area recovery. We reveal a strong, negative spatial relationship between old-growth forest loss and recovery by secondary forests, showing that regions with the greatest potential for large-scale restoration are also those that currently have the lowest recovery (e.g. Brazil dominates deforestation and emissions but has the lowest recovery). In addition, a temporal analysis of the regions that were >80% deforested in 1997 shows a continued decline in overall forest cover. Our findings identify three important challenges: (1) incentivising large-scale restoration in highly deforested regions, (2) protecting secondary forests without disadvantaging landowners who depend on farm-fallow systems, and (3) preventing further deforestation. Combatting all these successfully is essential to ensuring that the Amazon biome achieves its potential in mitigating anthropogenic climate change.