Abstract Farmers' management of bean diseases in the Great Lakes region of Africa was investigated from both phytopathological and anthropological perspectives. Local crop protection strategies were based on microclimate regulation, genetic diversity and sanitation. Microclimate management involved selectively integrating numerous agronomic practices depending on the site and conditions. The strategies included manipulating sowing density and time of sowing, choice of soil, use of varieties, variety and species mixtures for specific conditions, foliage reduction, staking and selective weeding. Decision‐making flexibility was essential to the effectiveness of local microclimate management strategies. Resistant varieties were available in local mixtures and were managed by farmers through intervention and natural selection in the field. A number of sanitation methods were used, such as removal of debris from fields at harvest, but their value by farmers in crop protection was less recognized. Improvements to local plant protection should be possible through the development of technologies which reduce losses in plant density, improve crop resistance to 'rain' while maintaining genetic variability and improve seed health, and by educating farmers in the basic principles of plant pathology while ensuring their participation in the development of technologies destined for their agroecosystems. The authors emphasize the importance of developing technologies for fanners which do not decrease existing management flexibility.