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Significance For decades, Amazon indigenous peoples and local communities (IPLCs) have impeded deforestation and associated greenhouse gas emissions. While emissions inside indigenous territories (ITs) and protected natural areas (PNAs) remain well below levels outside, unsustainable forest clearing is on the rise across the nine-nation region. In addition, Amazon ITs and PNAs are increasingly vulnerable to the less conspicuous (and often-neglected) processes of forest degradation and disturbance, which diminish carbon storage and ecological integrity. The trend toward weakening of environmental protections, indigenous land rights, and the rule of law thus poses an existential threat to IPLCs and their territories. Reversing this trend is critical for the future of climate-buffering Amazon forests and the success of the Paris Agreement., Maintaining the abundance of carbon stored aboveground in Amazon forests is central to any comprehensive climate stabilization strategy. Growing evidence points to indigenous peoples and local communities (IPLCs) as buffers against large-scale carbon emissions across a nine-nation network of indigenous territories (ITs) and protected natural areas (PNAs). Previous studies have demonstrated a link between indigenous land management and avoided deforestation, yet few have accounted for forest degradation and natural disturbances—processes that occur without forest clearing but are increasingly important drivers of biomass loss. Here we provide a comprehensive accounting of aboveground carbon dynamics inside and outside Amazon protected lands. Using published data on changes in aboveground carbon density and forest cover, we track gains and losses in carbon density from forest conversion and degradation/disturbance. We find that ITs and PNAs stored more than one-half (58%; 41,991 MtC) of the region’s carbon in 2016 but were responsible for just 10% (−130 MtC) of the net change (−1,290 MtC). Nevertheless, nearly one-half billion tons of carbon were lost from both ITs and PNAs (−434 MtC and −423 MtC, respectively), with degradation/disturbance accounting for >75% of the losses in 7 countries. With deforestation increasing, and degradation/disturbance a neglected but significant source of region-wide emissions (47%), our results suggest that sustained support for IPLC stewardship of Amazon forests is critical. IPLCs provide a global environmental service that merits increased political protection and financial support, particularly if Amazon Basin countries are to achieve their commitments under the Paris Climate Agreement.