In this paper we detail and contextualise the collaborative participatory research process developed throughout the IMMERSE research project which maps the integration of migrant children in education in Europe. We begin with a brief overview of IMMERSE and thereafter discuss the research design with reference to literature on collaborative research approaches and on working with children and young people’s research advisory groups. IMMERSE involved a large-scale data collection with over 24,000 children and young people in six countries and such large-scale data collection presents a challenging context in which to include children as collaborators and influencers in the research process. We demonstrate how, drawing on existing knowledge as well as our own experiences of working with children as research partners, we developed innovative ways of ensuring children’s voices were integral to and embedded in the research at various points of the process. Throughout the duration of the project, we developed several strategies to ensure that children were involved as research partners and influencers. To ensure children and young people’s active involvement and influence on the research, a Children and Young People’s Advisory Group was established at the beginning of IMMERSE which was composed of 18 migrant and refugee children resident in Ireland. This group acted as an expert group, to reflect on the experiences of migrant children and represent their peers in this process. In addition, children across the six IMMERSE countries were involved in the design and validation of the dashboard of socio-educational integration indicators and the ensuing research instruments.