Agro-enterprise development initiatives are being promoted to empower women, who make up the biggest portion of the marginalized groups in most rural societies to achieve gender equity. The complexity and nature of gender inequalities within this sector raise questions as to whether these initiatives are achieving their intended purpose. The main concern is the relationship between agro-enterprise development and gender equity. The study makes systematic investigations and analysis of how the current state of gender equity in northern Uganda is influencing the development of agro-enterprises and how their development is influencing gender equity. Insights from the study provides valuable information about critical issues to consider in ensuring effective women empowerment. Structural elements such cultural norms, and the inability of men to provide for their households due to poverty were identified as the major causes of such tensions which were reinforcing gender inequities. Improved co-operation between spouses and the flexibility of men in rich male headed household were factors that were contributing to increased women's empowerment through agro-enterprise development.