Agroforestry systems (AFS) are management schemes where trees are often combined with crops, pastures, and occasionally fauna. The production process of these systems can be assessed using eco-friendly indicators based on energy consumption, production, greenhouse gas (GHG) emissions, and water usage, which can provide insights into the environmental impacts of these agroforestry (AF) schemes. Based on a literature review, we found that AFS could help reduce the high inputs of non-renewable energy associated with agriculture, as well as mitigate GHG emissions. Tree-based systems can generate electricity and bioenergy at scales suitable for both domestic and industrial use, even though farming activities may have some negative environmental impacts. Water is a critical resource for the sustainability of AFS. However, AF practices during different stages of production, transport, and distribution are some of the variables that can improve input management and reduce water footprint. Proper management can improve water quality, decrease water usage (e.g., for livestock), and reduce the amount of water required for production. On the other hand, AFS has the advantage of storing significant quantities of carbon (C), ranging from 12 to 220 tC per hectare, which contributes greatly to climate change mitigation. The net GHG mitigation from AFS is estimated at 27.2 t CO2 per hectare per year. With the high potential for C stocks in AFS, these systems offer an opportunity within the C credit mechanism. Carbon sequestration through AF is increasingly seen as an alternative financial opportunity for climate change mitigation, as the C stocks in AFS can be measured, and the resulting C credits can be sold to companies or individuals seeking to offset their GHG emissions. The implementation of AFS in the context of C credits based on energy and water footprints is not standardized, as it varies depending on specific AF practices. Methods to improve energy efficiency and reduce the reliance on fossil energy sources are essential for ensuring a sustainable energy supply. In conclusion, estimating C and energy footprints can help producers reduce their GHG emissions in a cost-effective manner. These assessments can serve as tools for managing production in AFS, contributing to both environmental sustainability and climate change mitigation.