This paper addresses to compare complex systems analysis methodologies that include social and ecological features of interaction between them and at various scales, to be applied in the analysis of forestry projects. This kind of projects, labeled under climate change mitigation mechanisms as clean development mechanism (CDM) and voluntary carbon markets (VCM), arise interest to study the benefits they can achieve at the “developing countries”. Literature on benefits through forest CDM projects was reviewed and analyzed under three methodologies: Institutional Analysis and Development (IAD), Socio-Ecological Systems (SES) and Co-Evolutionary Systems (CES). The combined use of these methodologies has contributed to a better understanding of the type of interactions and emerging processes within forestry projects; there were identified also common features of the methodologies and some interacting elements within projects relevant to the benefit deployment. The paper concludes that the implementation of carbon sequestration forestry projects requires institutional, biophysical and social elements to satisfy stakeholders and their analysis requires methodologies that recognize those features. Besides, studied methodologies have sufficient common features to be used jointly to represent forest projects processes. It is identified the necessity of further research in methodology or in applied models, specifically on agent-based modeling.