Water, energy, and food are essential elements for human life, but face constant pressure resulting from economic development, climate change, and other global processes. Predictions of rapid economic growth, increasing population, and urbanization in the coming decades point to rapidly increasing demand for all three. In this context, improved management of the interactions among water, energy, and food requires an integrated “nexus” approach. This paper focuses on a specific nexus case: biogas generated from organic waste, a renewable source of energy created in livestock production, which can have water-quality impacts if waste enters water bodies. An innovative model is presented to make biogas and biomethane systems feasible, termed “biogas condominiums” (based on collective action given that small- and medium-scale farms on their own cannot afford the necessary investments). Based on the “farm to fuel” concept, animal waste and manure are converted into electrical and thermal energy, biofuel for transportation, and high-quality biofertilizer. This nexus approach provides multiple economic, environmental, and social benefits in both rural and urban areas, including reduction of ground and surface water pollution, decrease of fossil fuels dependence, and mitigation of greenhouse gases emissions, among others. The research finds that biogas condominiums create benefits for the whole biogas supply chain, which includes farmers, agroindustry, input providers, and local communities. The study estimated that biomethane potential in Brazil could substitute the country’s entire diesel and gasoline imports as well as 44% of the total diesel demand. In the United States, biomethane potential can meet 16% of diesel demand and significantly diversify the energy matrix.