Land is an essential natural resource for climate mitigation and peace. It is commonly connected with sources of GHG emissions and with drivers of (violent) conflict. Therefore, climate mitigation and peacebuilding strategies are co-designing sustainable land-use systems (SLUS) with affected communities to integrate land-based climate mitigation and peacebuilding objectives. SLUS is practiced within agricultural production systems that meet sustainability principles (environmental, social, and economic). Nevertheless, there needs to be more program evaluation frameworks, especially measurable indicators, that integrate these two objectives (achieving peace and climate mitigation). This study aims to develop a methodology and criteria to evaluate the precise mechanisms of SLUS influencing greenhouse gas (GHG) emissions and drivers of conflict. A mix-method approach was used in two case study regions, Cesar and Caquetá, Colombia, where SLUS strategies where implemented. First, we conducted three workshops, two in-person and one virtual (n = 103). Secondly, we held semi-structured interviews (n = 115) to make an analysis of the conflict. Our research focused on the drivers of land-based emissions and conflict drivers targeted by the SLUS implementation. Lastly, through a household survey (n = 929), we illustrated the impacts of SLUS in peacebuilding at the farm level. Results show that SLUS, such as cocoa agroforestry, can contribute to climate change mitigation and deliver co-benefits in four core factors: (i) socio-economic inclusion by creating jobs and diversifying livelihoods, (ii) dialogue and conflict transformation by allowing negotiations around the participatory design of farms, including conservation agreements, (iii) natural resource governance, and (iv) cooperation by creating knowledge exchange and a community of practice.