Background: There has been substantial progress in research on preventing violence against women and girls (VAWG) in the last 20 years. While the evidence suggests the potential of well-designed curriculum-based interventions that target known risk factors of violence at the community level, this has certain limitations for working in partnership with communities in low- and middle-income (LMIC) countries, particularly when it comes to addressing the power dynamics embedded within north-south research relationships. Methods: As an alternative approach, we outline the study design for the EVE Project: a formative research project implemented in partnership with community-based researchers in Samoa and Amantaní (Peru) using a participatory co-design approach to VAWG prevention research. We detail the methods we will use to overcome the power dynamics that have been historically embedded in Western research practices, including: collaboratively defining and agreeing research guidelines before the start of the project, co-creating theories of change with community stakeholders, identifying local understandings of violence to inform the selection and measurement of potential outcomes, and co-designing VAWG prevention interventions with communities. Discussion: Indigenous knowledge and ways of thinking have often been undermined historically by Western research practices, contributing to repeated calls for better recognition of Southern epistemologies. The EVE Project design outlines our collective thinking on how to address this gap and to further VAWG prevention through the meaningful participation of communities affected by violence in the research and design of their own interventions. We also discuss the significant impact of the COVID-19 pandemic on the project in ways that have both disrupted and expanded the potential for a better transfer of power to the communities involved. This article offers specific strategies for integrating Southern epistemologies into VAWG research practices in four domains: ethics, theories of change, measurement, and intervention design. Our aim is to create new spaces for engagement between indigenous ways of thinking and the evidence that has been established from the past two decades of VAWG prevention research and practice.