A paradigm shift is required to transform current natural resource management (NRM) in Indonesia’s decision to move into low-carbon development to achieve the greenhouse gas emission target. No study has been conducted to assess whether or not the current approaches are reliable in anticipating the conundrum of the new juncture. We reviewed 10 cases of NRM practices in Indonesia from 2019–2023 collected from the Scopus dataset by integrating the prisoner’s dilemma approach into the socio-ecological framework to analyze the practices and the anticipated gaps. Our finding revealed that socio-economic governance is the dominant view in interpreting the competition between personal and collective interests in NRM. Seeing NRM as an allocation problem and the excessive use of the legal normative approach in interpreting and addressing the problem are flaws in the approach. Combining the prisoner’s dilemma approach with the socio-ecological governance framework enabled us to address the flaws. Promoting polycentric governance that accommodates social trust, reciprocities, and socio-ecological beliefs and reduces uncertainties about ownership and the resources necessary to reduce defective behavior is a solution to transform the structure of the competition. Revising the socio-economic payoff into a socio-ecological value-oriented institution is the strategy to address the conundrum.