Much of the worlds’ annual harvest loss to pests and diseases occurs as a consequence of crops grown in monocultures, or cultivated varieties with uniform resistance. This uniform resistance is met by the continuing evolution of new races of pests and pathogens that are able to overcome resistance genes introduced by modern breeding, creating the phenomenon of boom and bust cycles. One of the few assets available to small-scale farmers in developing countries to reduce pests and diseases damage is their local crop varietal diversity, together with the knowledge to manage and deploy this diversity appropriately. Local crop varietal diversity of banana and plantain (Musa spp.) and common bean (Phaseolus vulgaris) was measured at the community and household levels within farmers’ fields in four agro-ecological areas of Uganda. Resistance of traditional and modern varieties of P. vulgaris to anthracnose, angular leaf spot, and bean fly and of traditional and modern varieties of Musa spp. to black sigatoka, banana weevils and nematodes was assessed from participatory diagnostics of farmer knowledge and cross-site on-farm and on-station trials. By performing cross-site on-farm experiments, it was possible to identify traditional varieties with higher resistance to pest and diseases when grown outside their home sites. Increased diversity of crop varieties, measured by number of varieties (richness) and their evenness of distribution, corresponded to a decrease in the average damage levels across sites and to a reduction of variance of disease damage. In sites with higher disease incidence, households with higher levels of diversity in their production systems had less damage to their standing crop in the field compared to sites with lower disease incidence. The results support what might be expected of a risk-minimizing strategy for use of diversity to reduce pest and disease damage.