I explored Jatropha curcas growth and yield in Indonesia using agroforestry models developed by World Agroforestry centre (ICRAF) – Bogor, Indonesia. The models were tools used to estimate above and belowground biomass, and seed yield in relation to stem base and proximal root diameters. This reduces the need for destructive sampling to determine biomass. Seed yield across the three cropping systems tested; monoculture, intercropping, and hedge can be predicted using plant height and the number of productive twig/branch, although the number of inflorescence clusters per productive twig may be important. This indicates that across the different cropping systems age and management of pruning and fertiliser influenced yields. Jatropha leaf mulch as a source of organic nutrients, canopy pruning to reduce aboveground competition, and root pruning to reduce belowground competition were all found to influence jatropha and maize yields. My results show that there were yield trade-offs in jatropha-maize intercropping system.