With the introduction of the African Continental Free Trade Area (AfCFTA), there are expectations to boost interregional trade amongst other measures to increase interregional integration. In particular, the agricultural sector is anticipated to be an important beneficiary of the strengthening and development of interregional linkages from the advent of the AfCFTA. In our paper, we focus on the fruit and vegetables sector, and we implement a new extension of the MAGNET model (Modular Applied GeNeral Equilibrium Tool), a global computable general equilibrium (CGE) model, which has theoretical adaptions in order to model trade flows at the disaggregate HS-level. Fruits and vegetables are high-value crops, which many African countries are switching towards, diversifying their agricultural portfolios away from typical cash crops. In addition, while in many current standard CGE frameworks there is a single aggregate commodity “Veg & Fruit”, in reality, the composition of the underlying products within this aggregate commodity can vary significantly. For this analysis we compare two scenarios: (1) a simulation of AfCFTA with the standard MAGNET model and (2) a simulation of AfCFTA with the HS-level modelling extension. Preliminary simulation results indicate a high difference between the two scenarios in terms of trade flows originating from Southern Africa which depend on several factors, including the tariff shock at the HS- versus GTAP- level, the underlying value of trade from Southern Africa, and the differing theoretical structure of the HS module.