Northern Uganda's post-conflict agricultural landscape presents both acute challenges and significant opportunities for sustainable rural development. This study examines the effect of agro-ecological practices on the income and sustainability outcomes of smallholder farmers in Nwoya District, a key agricultural zone in Northern Uganda. A quasi-experimental design was employed, comparing outcomes between 160 smallholder farmers who adopted agroecological practices through a structured intervention program and 160 control farmers using conventional agricultural methods. Data were collected at baseline (2021) and endline (2023), measuring household income, crop yield, soil health, input costs, and ecological resilience indicators. Results indicate that farmers adopting agro-ecological practices experienced a 38.4% increase in net household income, a 27.1% improvement in crop yield diversity, and significant improvements in soil organic matter content compared to control farmers. Adoption was associated with a 41.2% reduction in external input costs, primarily through reduced fertilizer and pesticide expenditure. Structural barriers to adoption, including limited access to technical knowledge, short-term income trade-offs during transition periods, and inadequate market access for organically certified produce, were identified. The study provides robust evidence for scaling agro-ecological approaches in Northern Uganda's post-conflict agricultural development agenda.