In this work, we merge socio-economic data with data on deforestation to explore the interrelationship between rural migration, the development of commercial agricultural sector, and forest cover loss. Specifically we test the role of cash crop producers and inter-district migrants on the tree loss in the parish of residence, while controlling for several other household-level and parish-level contributing factors of deforestation, including population density, proximity to markets and protected areas. Also, we investigate the agricultural channel, specifically producing cash crops, as one major channel through which inter-district migration affects deforestation. Our analysis aims to support the identification of policy strategies to reduce the adverse impacts of agricultural commercialization initiatives on Uganda’s critical natural resources; and identify policy options that maximize migrant’s benefits on recipient areas while minimizing downside risks of migration related to over-exploitation of resources and deforestation.