Regrowth and planted trees in agricultural landscapes are rarely protected from clearing under national Forest Acts. There is, therefore, some question over the long-term security of any value they might provide to biodiversity and the global carbon cycle. Engaging landholders in carbon credits that are conditioned on planted areas being maintained into the future could improve the situation. To begin carbon trading, landholders need precise and accurate estimates of the carbon sequestered by the trees in their fields. Accurate estimates of carbon stocks depend to a greater degree on the availability and adequacy of the allometric equations that are used to estimate tree biomass. The present study has developed an allometric model for estimating the woody biomass of Jatropha trees planted as boundary hedges in agricultural landscapes under smallholder farming systems in Malawi. The predictive performance of the model was assessed and was subsequently compared with the published Jatropha models. The results showed that the statistical fits of our model were generally good, enabling one to use it with confidence for estimating wood biomass in Jatropha stands from which they were derived. The published Jatropha models consistently overestimated the woody biomass by as much as 55%, rendering them unsuitable for application in estimating woody biomass in our study sites.