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In Colombia’s post-conflict territories, restoring degraded landscapes while promoting sustainable livelihoods is a critical challenge. This study evaluates the environmental co-benefits of agroforestry systems based on Hevea brasiliensis (natural rubber) in the departments of Caquetá, Guaviare, and Meta. Using a mixed-methods approach that combines spatial analysis, carbon sequestration modeling (IPCC Tier 1), literature review, and policy diagnostics, the study compares rubber agroforestry with monoculture systems and degraded land use. Results show that rubber-based agroforestry can sequester up to 110 Mg C ha⁻¹ over a 25-year period, up to 40% more than monocultures, and significantly enhance biodiversity indicators such as understory plant richness and avian diversity. Despite strong ecological potential, institutional and economic barriers persist, including limited technical support and market integration. Policy recommendations emphasize the need for coordinated agroforestry incentives, improved technical training, and integration into Colombia’s climate and post-conflict strategies. Rubber agroforestry thus emerges as a multifunctional land-use option that supports both ecological restoration and peacebuilding objectives.