In Brazil, the epicenter of the Zika crisis, brown, black, and indigenous poor women living in municipalities with scarce resources were disproportionally affected. The gendered consequences of the epidemic exposed how intersectional lenses are central to understand the impact of public health emergencies in the lives of women and girls. The demand for Zika-affected children and women to be research participants is relevant for an ethical analysis of participant protection procedures during a crisis. We investigated how women experienced research participation by analyzing their narratives. Two-year-long longitudinal qualitative study in Brazilian sites located in the epidemic’s epicenter was performed using mixed methods: ethnography with women from two distinct states and individual semi-structured interviews with five women in different Zika-affected states, four of which were community leaders. All women in the study were mothers or grandmothers of Zika-affected children. Thematic analysis was used for data evaluation. Women perceived being pressured to participate in research and a lack of benefit sharing. Structural determinants of gender inequality, such as its effect on power distribution, were found to impact research participant protection. Formal procedures for research protocols approvals were insufficient in protecting participants because these instruments were unable to account for structural aspects. Communitarian mobilization, through WhatsApp groups, was found to be an important mechanism to create conditions to challenge oppressive structures. Strengthening public health, effective community-based participation in research planning and implantation of ethical strategies that promotes gender equality can have transformative effect on unequal power structures and promote participant protection.