Jatropha curcas L. (JCL) commercial plantations in Mexico, one of the most important JCL origin centers, have failed due to a variety of biological, political and technical factors affecting their productivity. This study explores feasible sites of JCL cultivation as a potential source for biodiesel production in Mexico, given agroclimatic and agroecological considerations. We propose a GIS-based approach for estimating suitable and available lands to grow JCL by integrating an Analytical Hierarchy Process (AHP) in the ArcGIS software. Spatial analysis combined multiple data, different evaluation criteria, three land availability classes (high, medium and low potential) and took into account ecological, ethical, and political restrictions, and considering two scenarios with different restriction levels. Suitability and availability maps were generated using agroclimatic information (climatic, land use/soil, and climate change and extreme weather events risk) together with other socioeconomic factors. Approximately 15.3% of Mexican territory is available for JCL production yielding a biodiesel production of 9.683 Mm3/year. Amelioration of the available land is necessary to improve land selection. GIS-based analysis represents a first approach to establish a successful biodiesel project that avoids, competition with food or feed production, maintains biodiversity conservation, and promotes biofuel supply chain development. This procedure would also be applicable to other energy crops such as oil palm and Ricinus communis.