The Mexican neoliberal political regime created a hegemonic governance model (top-down) which has tried to impose a single definition for the rules of the distribution of the costs and benefits (environmental and economic) related to the appropriation of “natural resources” (fossil fuels, forests, mineral, water, genetic). Social metabolism is a framework that highlights the contribution of indigenous communities in their struggles to build a movement of environmental justice and austerity (a regionally sensitive alternative to degrowth). By forging an indigenous communitarian identity, known as comunalidad in the Sierra Juárez of Oaxaca, they are forging a new form of “bottom-up” governance. We designed key components and indicators to understand the social metabolism related to three policy objectives: a) local governance; b) reducing water vulnerability; and c) social justice. Heterodox perspectives by Marx and Illich enrich the analysis. The analysis emphasizes the importance of the social control of the “tools” needed to protect their communities and their heritage, transforming the institutions that were imposed on them. The approach is critical for constructing a research program in “ecological economics from below.”