A jatropha-based whole-crop biorefinery was designed and assessed under the sustainability framework developed by Sacramento-Rivero (2012, http://dx.doi.org/10.1002/bbb.335). This framework involves techno-economic analysis, along with environmental life cycle assessment, and non-renewable energy and water consumption, into a set of indicators whose values are normalized and range between cero to infinity. Indicators that range between 0 and 1 are considered sustainable. The indicators are gathered into 5 categories including renewability, economics, fossil-based products displacement, biodiversity protection, environmental mitigation, and community development. Information regarding the cultivation of jatropha was collected from local jatropha plantations and two potential scenarios to harness the jatropha biomass were identified, simulated, and assessed. The first scenario (BPP) refers to a standalone biodiesel production process which does not harness the lignocellulosic residual biomass, while the second (IBP-2) uses it for producing bio-oil, bio-char, and the internal heat and power requirements. Results indicate that the biorefinery scenario (IBP-2) performs better than the standalone biodiesel production (BPP) due to a more diverse portfolio of products allowing for a better sustainability performance. However, the use of pesticides and fertilizers, along with an intense water consumption for the jatropha crops, make the system unsustainable in the fossil-based products displacement and environmental-mitigation categories. In fact, the agricultural stage also contributes the most (77%) to the total production cost, environmental load (more than 60%), non-renewable energy consumption (66%), and water consumption (99%).