In Uganda, despite government support, many farmer organizations are short-lived or exist solely to receive subsidies. Existing literature evaluates the sustainability of farming systems, technology impacts, and non-certified markets, yet a gap remains regarding the sustainability of farmer organizations. This study addresses this gap by determining a sustainability index and the effect of organizational and institutional factors on the sustainability of farmer organizations in central and northern Uganda. It highlights how regional disparities impact organizational sustainability. Using cross-sectional data from 272 farmer organizations across 12 randomly selected districts, a multilevel mixed-effects linear regression in Stata13 was employed. Results indicate that Ugandan farmer organizations have a low sustainability index of 36%, with central organizations slightly outperforming northern counterparts by 2%. Significant differences exist between northern and central organizations in terms of finances, resources, value addition, training, and leadership. Additionally, internal financial dependence, leadership committee size, farm management, and value addition training greatly enhance sustainability. Specifically, regional level variables contribute 21% to changes in the sustainability of farmer organizations in Uganda. To enhance sustainability, farmer organizations should engage in income-generating activities aligned with their economic, environmental, and social welfare objectives. The government should also intensify leadership, farm management, and value addition training.