In this study we analyze the capacity of agrobiodiversity to increase resilience of banana-based smallholders in Uganda as affected by disease incidence or climate change and associated price changes until 2050. We explore trade-offs and synergies by means of various indicators of economic, environmental and nutritional impact determined by selected cropping patterns. As a result of increased agrobiodiversity, in all scenarios considerable improvements could be achieved for almost all indicators, which results in higher farm resilience. Our results also indicate that climate change can increase vulnerability of smallholder farmers in Uganda with respect to their income, whereas banana disease can put pressure on nutrition and sustainability of production. Increasing revenues from cropping associated with a stronger focus on a small number of profitable crops would come with a trade-off due to increased vulnerability to yield and price fluctuations. When it comes to crop diversification, it has a significant positive impact on soil health, especially soil erosion, and nutrition. Our analysis of correlations between areas of different crops and the performance indicators reveals a further layer of trade-offs at crop level. In particular, under baseline scenario yam leads as an income-generating crop, with high vitamin A yield but with negative consequences to environment and high revenue instability.