Health professions education (HPE) research in the General Practice domain (GP-HPE) is vital for high-quality healthcare. Collaboration among GP-HPE researchers is crucial but challenging. Formulating a research agenda, involving stakeholders, and fostering inter-institutional collaboration can address these challenges and connect educational research and practice. We used Q-methodology to explore perspectives on GP-HPE research of participants from all Dutch postgraduate GP training institutes. Participants individually sorted statements based on the relevance of future GP-HPE research for educational practice. Data analysis comprised inverted factor analysis, rotation, and qualitative interpretation of configurations of all statements. The National Meeting on Educational Research took a participatory approach. We included 73 participants with diverse involvement in GP-HPE research. We identified five distinct perspectives, each representing a research focus area for developing and innovating GP education: the clinician scientist, the socially engaged GP, the specific GP identity, the GP as an entrepreneur, and the GP engaged in lifelong learning. The resulting five perspectives align with General Practice hallmarks. Q-methodology and a participatory approach facilitated collaboration among stakeholders. Successful inter-institutional collaboration requires a common goal, neutral leadership, participant commitment, regular meetings, audit trail support, process transparency, and reflexivity. Future research should address evidence gaps within these perspectives. Using Q-methodology turned out to be valuable for compiling a national research agenda for GP-HPE research. The research process helped to cross boundaries between researchers in different institutions, thus putting inter-institutional collaborative advantage center stage. Our approach could provide a conceivable procedure for HPE researchers worldwide.