For over 20 years, ACIAR, CSIRO and Indonesian agencies have collaborated on research to understand and effectively manage tuna species harvested by Indonesian fisheries. The long-term collaboration reflects the importance of highly migratory tunas as a shared fishery resource within Indonesia, Australia and the Indo-Pacific region. Indonesia is the world’s largest producer of tuna and a member of three regional fisheries management organisations. Small-scale and commercial tuna fisheries support Indonesia’s economy, local livelihoods and food security. In Australia, tunas underpin important national and regional fisheries and aquaculture industries. We reviewed the engagement in tuna fisheries research and capacity building that has strengthened the evidence-base for sustainable management of Indonesian fisheries. Multidisciplinary approaches, strong partnerships with complementary initiatives, trusted relationships, and extension to fishery stakeholders and policy makers have been central to the translation of the science into policy to respond to shared challenges. The positive impacts within Indonesia and regionally, have been multidimensional, including supporting development of the National Tuna Management Plan and the achievement of market-based certification for a small-scale Indonesian fishery. Future opportunities for impactful collaboration should continue the multidisciplinary focus, support implementation of the Harvest Strategy Framework and include an increased emphasis on climate-related impacts.