Given the challenges facing African agriculture resulting from climate-induced stresses, building resilience is a priority. Seed systems are important for enhancing such resilience as seed security has direct links to food security, and resilient livelihoods in general. Using data from a case study in West Nile region in Uganda, we studied practices in farmer seed systems and decisions, particularly in response to climate-induced stress. Results helped to generate recommendations for enhancing seed system resilience. We used social-ecological framework and multinomial logit model to analyze seed systems and factors influencing farmers' decisions about seed use respectively. Farmers ranked drought as the most important climate factor affecting crop production. With over 50% of farmer seed sourced on farm, the effect of climate factors on seed system functioning was perceived in relation to diminishing levels in quantity and quality of yield. Decline in yield affected farmer seed saving, increased grain prices due to high demand, affecting seed availability and affordability. The relative importance of seed sources varied during normal and stress periods, and by crop. Farmers tended to shift from farm-saved seed to social networks and local markets during stress periods. Local Seed Businesses emerged as an alternative source of planting material during stress periods. Formal seed enterprises were important in delivering improved seed, especially for maize, though their importance during stress periods diminished. Farmer characteristics and ecological factors played a role in defining the type of seed used, though their significance varied by crop. We recommend an approach that integrates farmer seed systems with the formal system in general, but specifically focusing on strengthening social networks, promoting farmer seed enterprises and crop adaptation practices at farm scale.