Indigenous Territories (ITs) and Community Managed Protected Areas (PAs) with less restriction on forest use than integral PAs may represent cost-effective natural climate solutions to meet the Paris agreement. However, the literature has been limited to examining the effect of ITs and Community Managed PAs on deforestation, despite the influence of anthropogenic degradation. Thus, little is known about the temporal and spatial effect of allocating ITs and Community Managed PAs on carbon stocks dynamics that account for losses from deforestation and degradation. Using Amazon Basin countries and Panama at the national level, and Petén (Guatemala) and Acre (Brazil) at the subnational level, this study aims to estimate the temporal and spatial effects of ITs and PAs on carbon stocks. To estimate the temporal effects, we use annual carbon density maps, matching analysis, and linear mixed models. Furthermore, we explore the spatial biases derived from matching analysis and use geographic discontinuity designs to assess the spatial effect of PAs and ITs boundaries on carbon stocks. The temporal effects highlight that allocating ITs preserves carbon stocks and buffer losses as PAs in Panama and Amazon Basin countries. Community Managed PAs temporal effect on carbon stocks surpasses that of integral PAs in Petén (Guatemala) and Acre (Brazil). The geographic discontinuity designs reveal that ITs and Community Managed PAs boundaries secure more extensive carbon stocks than their surroundings, and this difference tends to increase towards the least accessible areas. These results also suggest that indigenous and community land-use in neotropical forests may have a limited and stable spatial impact on carbon stocks. Our findings imply that ITs and Community Managed PAs in neotropical forests support Nationally Determined Contributions (NDCs) under the Paris Agreement. Thus, Indigenous peoples and local communities must become recipients of countries’ results-based payments.