Post-conflict era in Colombia after the enactment of the peace agreements between the government and armed groups has caused a growing interest in the social, environmental and economic needs of the communities affected by armed conflict, today known as "collective reparation subjects". This interest is perceived through the continuous calls by national and local governments to companies and the scientific community, which seek to contribute to the regional challenges in terms of environmental conservation, biodiversity, and peacebuilding within these communities. Considering this new scenario, selection and decision-making processes on this issues need to be transformed, so that, in addition to selecting the best projects, the community is actively involved, thus generating benefits related to social learning and knowledge appropriation. Therefore, the aim of this research is to propose a methodology that involves different scientific methods for enabling community participation and knowledge construction on social, environmental and economic dynamics, in order to incorporate the analysis of information directly obtained from communities in decision-making processes for the selection of green projects. For the development of the proposed methodology for green projects assessment and prioritization, we suggest the integration of dynamic systems modeling, participatory modeling and the analytical network process (anp). With our results, we expect to contribute from a scientific perspective to the development of a sustainable and participatory model that can be applied in decision-making processes. In addition, from a practical approach, we expect this work facilitates decision-making in the selection processes of green projects taking place in post-conflict areas in Colombia.