Driven by the need to develop a wide variety of products with low environmental impact, biorefineries need to emerge as highly integrated facilities. This becomes effective when overall mass and energy integration through a centralised utility system design is undertaken. An approach combining process integration, energy and greenhouse gas (GHG) emission analyses is shown in this paper for Jatropha biorefinery design, primarily producing biodiesel using oil-based heterogeneously catalysed transesterification or green diesel using hydrotreatment. These processes are coupled with gasification of husk to produce syngas. Syngas is converted into end products, heat, power and methanol in the biodiesel case or hydrogen in the green diesel case. Anaerobic digestion of Jatropha by-products such as fruit shell, cake and/or glycerol has been considered to produce biogas for power generation. Combustion of fruit shell and cake is considered to provide heat. Heat recovery within biodiesel or green diesel production and the design of the utility (heat and power) system are also shown. The biorefinery systems wherein cake supplies heat for oil extraction and seed drying while fruit shells and glycerol provide power generation via anaerobic digestion into biogas achieve energy efficiency of 53 % in the biodiesel system and 57 % in the green diesel system. These values are based on high heating values (HHV) of Jatropha feedstocks, HHV of the corresponding products and excess power generated. Results showed that both systems exhibit an energy yield per unit of land of 83 GJ ha-1. The global warming potential from GHG emissions of the net energy produced (i.e. after covering energy requirements by the biorefinery systems) was 29 g CO2-eq MJ-1, before accounting credits from displacement of fossil-based energy by bioenergy exported from the biorefineries. Using a systematic integration approach for utilisation of whole Jatropha fruit, it is shown that global warming potential and fossil primary energy use can be reduced significantly if the integrated process schemes combined with optimised cultivation and process parameters are adopted in Jatropha-based biorefineries.