Jatropha curcas is an oil-bearing semi-evergreen shrub or small tree with potential as a source of sustainable biofuel, yet information regarding vegetative and fruit biomass in relation to plant architecture is lacking. Research conducted in Indonesia used the tree based functional branch analysis (FBA) model as a non-destructive method to estimate above and belowground biomass, and plant architecture. The FBA utility for shrubs was unknown and required modification. This research used destructive measurements to validate modifications to the FBA model that included sub-categorisation of the tapering coefficient for twig, branch, and wood diameter classes, and addition of a fruit load parameter in the distal link. The modified FBA model confirmed jatropha to be a shrub rather than a tree, producing variable estimates for aboveground biomass. This variation was due to morphological plasticity in the length–diameter relationship of the branches that diverged from fractal branching architecture. Fruit biomass variation between replicates was not well estimated and total proximal root diameter was a poor predictor of total root biomass, due to the proximal roots having enlarged water storage structures that do not follow fractal branching assumptions. Jatropha fruit was shown to predominate on twigs with a diameter between 0.9 and 1.4 cm. Understanding the correlation between fruit development and plant architecture will be necessary for fine-tuning the FBA model for future commercial breeding and selection. The high degree of morphological plasticity displayed by jatropha requires consideration when determining plant biomass.