Specialization in labor-intensive export crops, such as organic cocoa, can exacerbate gender inequality if production and revenues fall under men’s control and the additional labor burden falls on women. However, evidence on the implications for women’s empowerment in value chains that combine certification with other supply chain initiatives remains limited, particularly outside of West Africa. Using gender-disaggregated data from cocoa farm households in Peru, we examine how participation in certified organic cocoa production is associated with the intra-household division of labor and domains of women’s empowerment within the so-called sustainable segment of the value chain. We find that in certified organic cocoa farming households, women spend more time working on farm and in cocoa-related activities. However, this does not translate into an overall increase in their workload, as we find that women in certified households are less likely to have an off-farm occupation. We complement the analysis on women’s time use by exploring women’s time-use agency by certification status, confirming that overall workload varies by gender, yet not with certification. Furthermore, we show that women’s increased participation in organic production is associated with greater decision-making power around cocoa farming. At the same time, our findings reveal that women in certified organic households are less likely to have an individual income. Hence, we recommend that initiatives for environmentally sustainable cocoa production consider the intra-household labor division and time-allocation inequities to better integrate gender equality into their strategies.