The far-reaching impacts of the COVID-19 pandemic and recent environmental disasters have resulted in incredible challenges for Australian schools and for those committed to rigorous, high quality research in education. Well before the start of the pandemic, we began the ambitious task of running the largest randomised controlled trial (RCT) of its type in Australian education. Building on our previous research on the impact of the Quality Teaching Rounds (QTR) approach to teacher professional development, the RCT was designed to investigate effects of QTR on student achievement, on teachers and on the quality of teaching. In this paper, we detail key challenges and learnings from conducting such methodologically and logistically complex research while negotiating major environmental disasters and a global pandemic. Challenges in recruiting schools necessitated a split cohort design, with our first cohort of 125 schools affected by the late-2019 bushfires and then floods. Our second cohort of 80 schools was postponed from 2020 to 2021 due to the pandemic, with continuing impacts on the conduct of the research in 2021 from persistent COVID-19 outbreaks. Despite a rollercoaster of experiences before, during and after the height of the pandemic, we are on track to fully execute this ground-breaking research. High regard for the QTR intervention, ongoing support from our funding bodies and research schools, and the expertise and agility of our research team are contributing to ensuring the research remains rigorous and high quality while proceeding in a timely manner. In the current context of rapidly changing conditions and emerging challenges, we share our experiences and key learnings from running robust, high-quality research in schools. Particular attention is given to the importance of nurturing stakeholder relationships, navigating institutional constraints and conducting ongoing project evaluation and contingency planning. We share these insights in order to inform the broader educational research community and ultimately improve outcomes for our research partners.