In Uganda, the agricultural sector contributes substantially to gross domestic product. Although the involvement of Ugandan women in this sector is extensive, female farmers face significant obstacles, caused by gendering that impedes their ability to expand their family business and to generate incomes. Gender refers to social or cultural categories by which women–men relationships are conceived. In this study, we aim to investigate how gendering influences the development of business relationships in the Ugandan agricultural sector. To do so, we employed a qualitative–inductive methodology to collect unique data on the rice and cassava sectors. Our findings reveal at first that, in the agricultural sector in Uganda, inter-organization business relationships (i.e., between non-family actors) are mostly developed by and between men, whereas intra-organization business relationships with family members are mostly developed by women. We learn that gendering impedes women from developing inter-organization business relationships. Impediments for female farmers include their restricted mobility, the lack of trust by men, their limited freedom in communication, household duties, and responsibilities for farming activities up until sales. Our findings also reveal that these impediments to developing inter-organization business relationships prevent female farmers from being empowered and from attainting economic benefits for the family business. In this context, the results of our study show that grouping in small-scale cooperatives offers female farmers an opportunity to overcome gender inequality and to become economically emancipated. Thanks to these cooperatives, women can develop inter-organization relationships with men and other women and gain easier access to financial resources. Small-scale cooperatives can alter gendering in the long run, in favor of more gender equality and less marginalization of women. Our study responds to calls for more research on the informal economy in developing countries and brings further understanding to the effect of gendering in the Ugandan agricultural sector. We propose a theoretical framework with eight propositions bridging gendering, business relationship development, and empowerment and economic benefits. Our framework serves as a springboard for policy implications aimed at fostering gender equality in informal sectors in developing countries.