Research with ancient eDNA can build a more sustainable and secure food production system while also preserving biodiversity in cropping systems under climate change. However to maximise benefits to the planet and people, scientific research should be reciprocal in its approach, taking into account the priorities, needs and knowledge of those governing the lands, particularly Indigenous People. FREYJA will support local research partnerships and global governance frameworks to enter a new paradigm, which is curious and willing to learn from radically different perspectives. To support this vision, FREYJA sets out to investigate reciprocity in research, including new pathways for access and benefit sharing, with a particular focus on the context of ancient eDNA. Our international multidisciplinary team is committed to centering Indigenous methodologies, alongside the leadership and guidance of Indigenous communities to ensure our research is consistent with the UN Declaration on the Rights of Indigenous Peoples and Indigenous sovereignty. By combining ethico-legal parameters, cultural perspectives, and knowledge translation on research reciprocity, FREYJA’s findings will form a basis for capacity building and the development of a practical framework on research reciprocity that is tested, applied and reflected on with an eDNA scientific consortium.