Colombia is facing two crises: the effects of climate change, which has been intensified by deforestation. As well, the effects of the armed conflict, which weakens the social fabric and influences land-use changes. In Colombia and other territories affected by climate change and conflict, various farm-level agricultural interventions are being implemented to reduce deforestation for climate change mitigation, increase agricultural production, and contribute to peacebuilding. Some of these interventions include promoting sustainable land-use systems such as agroforestry systems, building peace, and reducing pressure on forests for climate action and biodiversity conservation. However, the effects of such interventions on climate change and peace are not yet fully understood. This research aims at assessing contributions to climate action and peacebuilding from agricultural interventions through an assessment framework. Specifically, we take two case studies of cocoa smallholders in priority areas for landscape restoration and carbon sequestration located in territories affected by the armed conflict in Colombia. We analyze if the implementation of cocoa cultivation in agroforestry systems reduces land-based greenhouse gas emissions while delivering peacebuilding. We classified a sample of 922 smallholders according to the complexity of their farming system along a gradient from a baseline system that does not incorporate agroforestry arrangements to an advanced agroforestry system with many timber and non-timber trees and a focus on organic fertilization and commercial practices. Economic results are compatible with ecological balance since more advanced systems also have a more significant potential for carbon sequestration, greater tree species diversity, and a high propensity for forest conservation. It is also noted that producers with advanced sustainable production systems feel that they have increased spaces for dialogue and cooperation and have reduced conflict over the use of and access to natural resources. To generate mobility of producers classified at the basic and intermediate levels to an advanced level it is necessary to strengthen the use of organic fertilizers and the implementation of better post-harvest practices. It is also necessary to generate incentives to establish conservation zones and plant shade trees.