Fair Trade and organic certification production of coffee and other commodities is popularly seen as beneficial to producers in many ways. However, gender analysis of Fair Trade is important for assessing the gains and losses for women and men specifically, which result from compliance with globally set codes of conduct. This article presents a case study of coffee production and trade in Uganda, aiming to do this. Producer organisations’ experience suggests that there is great need for gender equality issues to be integrated into all stages of coffee production and marketing – referred to as ‘value chains’ – if women are to realise prosperity from their labour, and to move up the value chain as active participants and decision-makers. Producer organisations need to develop strategies for addressing gender-specific constraints, and to build women's capabilities and confidence to aspire to positions and influence across the whole value chain. They should also seek to dismantle gender discrimination in the design, implementation, and monitoring of the wider certification code in coffee value chains.