This paper considers the contribution of North-South partnerships in conducting ethical and policy-relevant research in times of uncertainty. Using collaborative autoethnography, we critically reflect on our experience conducting two related research projects in Ethiopia during the COVID-19 pandemic. We discuss how our research has adapted to take account of changing policy priorities in response to the crisis, how we implemented careful research practices, and which strategies we adopted to ensure providing timely and quality evidence for the governments, schools and parents. Importantly, we reflect on how our North-South partnerships and our close engagement with the Ethiopian government play a pivotal role in overcoming the uncertainty caused by the pandemic and adapting our research to meet the needs of key stakeholders. Grounded in our reflections, we provide a set of guidelines to establish equitable research partnerships in times of uncertainty.