Coffee variety outweighs associated tree identity in modulating diseases and fruit load in the largest Robusta agroforestry system of Uganda

Robusta coffee in Uganda is traditionally cultivated under agroforestry systems, yet the role of associated trees in pest and disease regulation remains debated. Farmers increasingly question whether certain tree species exacerbate disease risks, while empirical evidence on tree–disease–productivity interactions remain scarce. We assessed the effects of associated tree identity, spatial arrangement, and coffee variety on major coffee diseases and fruit loads, based on a cross-sectional field survey in the Kaweri Coffee Plantation, Uganda’s largest Robusta coffee estate. Four dominant associated tree species—Mugavu, Jackfruit, Bark-cloth fig and Avocado—were selected across multiple Robusta varieties. Three major foliar diseases, i.e. coffee wilt disease (CWD), coffee leaf rust disease (CLR), and Brown-eye spot (BES) were monitored during the rainy season, when disease pressure peaks. Disease incidence was extremely high for CLR and BES, approaching 100%. Coffee variety was the strongest predictor of leaf CLR and BES incidence. By contrast, fruit load depended on complex interactions among tree species, tree–coffee distance, and coffee variety. Notably, fruit load per branch increased significantly near A. coriaria , while other tree species had neutral or negative effects. The relation between CLR and fruit load also varied among varieties. Our findings highlight the need for Robusta breeding programs to consider agroforestry conditions and tree–disease interactions, rather than relying on single-trait selection. Moreover, associated tree diversity, density, and spatial arrangement—as well as broader ecological factors such as soil fertility and biodiversity—likely modulate diseases and productivity, and should be integrated into future agroforestry recommendations.