This paper presents a qualitative case study of the experiences of student and community partners involved in collaborative health research in the context of an extra-curricular higher education science shop: Our Health. Our Health community partners set research questions around health and well-being, and conduct research with interdisciplinary groups of students using a community-based participatory research model. Our case study explores the benefits and challenges that this approach raises for students and community partners as they navigate the complexities of stepping beyond disciplinary boundaries and relationships to develop new research insights and methodologies. This qualitative case study draws on: grounded theory to analyse online focus groups with participating undergraduate students and community partners; semi-structured interviews with graduate students and key university staff members; and online project meetings. For the latter, we used non-participant observation to observe community members and students at work in online meetings, co-creating evolving knowledge around the lived experiences of health issues. Through these methods, we developed a deeper understanding of the relational modes of community–student collaboration in community-based participatory research. Our findings demonstrate the key role played by interdisciplinarity in the context of a community-based participatory research approach in enabling students and community partners to develop their intrapersonal skills, health research skills and knowledge integration skills, while strengthening connections between the academy and wider communities.