In recent decades, there have been considerable efforts to enhance, diversify, or implement alternative livelihood activities in marginalized coastal communities, to ease reliance on deteriorating coastal resources, reduce poverty and improve well-being outcomes. To date, gender has been notably absent from the literature on small-scale fisheries and associated livelihood improvement programs, despite increasing evidence of the importance of gender equality and women’s empowerment in achieving such outcomes in other contexts. In this paper, drawing from an evaluation of the effectiveness of 20 livelihood development projects implemented in coastal communities in Indonesia since 1998, we report on how gender was considered in these projects. We assessed whether and how gender was included in project rationales, and how men and women were included in project activities. We found that, despite the women being reached by many project activities, particularly efforts to increase women’s productive capacity through training and group-based livelihoods enterprises, 40% of the projects had no discernible gender approach and only two of the 20 projects (10%) applied a gender transformative approach that sought to challenge local gender norms and gender relations and empower women beneficiaries. Our assessment suggests the need for greater understanding of the role of gender in reducing poverty and increasing well-being outcomes in coastal communities. Lessons from comparable agricultural settings suggest that this may be facilitated by locally situated gender social relations analysis, integration of gender throughout livelihood improvement project cycles, gendered capacity building activities and shared learning from the evaluation of the gendered outcomes of project activities.