BACKGROUND: Tackling falsified and substandard medicines requires intersectoral collaboration, impact-oriented research and the effective application of research findings. However, the best way to organize research and involve stakeholders from different sectors to ensure that results are used, remains unclear. We aimed to assess how intersectoral stakeholder engagement in research on medicine quality in Indonesia evolved, influenced the research processes and participants, and affected the uptake of the results. METHODS: For this prospective case study, we adopted an abductive approach inspired by contribution mapping and collaborative governance. We conducted 37 interviews with key informants, observed 24 meetings and analysed 121 documents to systematically map the engagement of stakeholders in a study on medicine quality, focusing on processes, influences and research-related contributions. RESULTS: From the outset, it proved feasible, but challenging, to effectively engage stakeholders in research into falsified and substandard medicines in Indonesia. After a cautious start and persistent efforts, stakeholders, such as the national medicine regulatory authority, became increasingly involved and developed a shared understanding of the need for intersectoral collaboration to tackle problems with medicine quality. While the research findings did not lead to a different estimate of the magnitude of the problem, the involvement of stakeholders was beneficial. After formalizing the collaboration, stakeholders provided data needed to study potential risk factors, product varieties and sales volumes, and contributed to decisions during the research and interpretation of the findings. Owing to frequent personnel changes and diverging priorities, stakeholder engagement required more effort than anticipated, and necessitated a strategic and adaptive approach. This approach had to account for the varying priorities and interests of stakeholders, the evolving framing of the problem, the implications of the findings and the nature of the field, where regulators must operate cautiously, balance interests and respond to critical incidents. CONCLUSIONS: Intersectoral stakeholder engagement in medicine quality research is challenging but beneficial. Engagement contributed to building trust and relationships between researchers and stakeholders, helped forge an intersectoral network focused on medicine quality, exposed the medicine regulator to new methods, inspired stakeholders to take on new roles and make better use of existing data and furthered a research-policy partnership forum on pharmaceutical topics.