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Bananas on smallholder farmers in the African Great Lakes region are often pruned to illuminate shorter understory intercrops, reducing overall farm profitability. The impact of this practice on environmental and nutritional indicators are not known. This study determined the effect of this practice on operating profit, protein yield, soil organic matter (SOM) balance, and nitrogen input; and the management options for optimal performance of the intercrops. Alternative scenarios for improving soil nutrient balances of the system were also explored. Data from an experiment intercropping bush beans with banana at three leaf pruning levels (i.e., retaining all, seven, and four leaves) was used as the input for the multi-objective optimization FarmDESIGN model. Retention of four functional leaves mimicked a worst-case scenario observed on farms. Banana and bush bean monocrops served as controls. The model maximized operating profit, protein yield, and SOM, and minimized nitrogen input. Nutrient input scenarios in which (i) farmyard manure was only applied at planting (business as usual (‘BaU’)); and ‘BaU’, was combined with (ii) hedges, (iii) inorganic fertilizers, (iv) hedges and goat manure, (v) hedges and inorganic fertilizers, (vi) inorganic fertilizers and goat manure, and (vii) hedges, inorganic fertilizers, and goat manure, were also explored. Severe banana leaf pruning reduced profitability, SOM, and protein yield, although it’s less nutrient demanding. In contrast, the “un-pruned banana-bush bean intercrop” and “sole banana crop” had a higher profitability, SOM balance, and protein yield, whereas they demand more soil nutrients. No profound improvements in operating profit, SOM balance, and protein yield occurred for ‘BaU’, while hedges resulted in mild improvements. Profound improvements in all objectives occurred with the addition of the inorganic fertilizers, while goat manure resulted in a high SOM balance and N input. For ‘BaU’ and hedges, “severely pruned

Changes in land-use have been observed in banana-based systems in the African Great Lakes region affected by Xanthomonas wilt disease (XW) of banana. Through focus group discussions (FGDs) and the 4-cell method (to map the area under production and the number of households involved), changes in land-use were assessed in 13 XW-affected landscapes/villages along a 230 km transect from Masisi (where XW arrived in 2001) to Bukavu (XW arrived around 2014) in the Eastern Democratic Republic of Congo. Farmers' perceptions on the sustainability of new land uses were also documented. Soil nutrient content and erosion levels were measured for five major land-use options/trajectories on 147 fields across 55 farms in three landscapes along the transect. From banana being ranked the most important crop (92% of landscapes) before XW outbreaks, its importance had declined, with it grown on smaller farms by most households in 36% of the landscapes, while in 64% of cases by few households on smaller plots. Farmers uprooted entire banana mats or fields, expanding land under other crops. Species richness did not change at landscape level, although 21 crops were introduced at farm level. Banana is, however, still perceived as more sustainable due to its multi-functional roles. Soils under banana had better chemical attributes, while high erosion levels (Mg ha−1 year−1) occurred under cassava (1.7–148.9) compared with banana (0.3–10.7) and trees (0.3–5.9). The shifts from banana could thus affect supply of key services and sustainability of the farming systems. This study offers a good basis for interventions in XW-affected landscapes.