Agriculture accounts for 5% of the entire energy used worldwide. Most of it is not in a renewable form, so it can be linked to greenhouse gas emissions. According to the Paris Agreement, on climate change, one of its major targets is the reduction of greenhouse gas emissions. Therefore, the agricultural production process must drastically change. Currently, the sustainable use of water is critical for any agricultural development. Agricultural production effects water quality and sufficiency, as well as, freshwater wetlands. Energy balance, carbon, and water footprint are crucial for sustainable agricultural production. Agroforestry systems are important in reducing high inputs of non-renewable energy and greenhouse gas emissions, along with better water use, leading to the most minimal influence on climate change. Energy analysis, carbon, and water footprint can be applied to agroforestry systems’ production. An outline could be applied by adopting a modified—for agricultural production—life cycle assessment methodology to assess energy use, greenhouse gas emissions, and water consumption in agroforestry ecosystems.