BACKGROUND: Since climate change, pandemics and population mobility are challenging healthcare systems, an empirical and integrative research to studying and help improving the health systems resilience is needed. We present an interdisciplinary and mixed-methods research protocol, ClimHB, focusing on vulnerable localities in Bangladesh and Haiti, two countries highly sensitive to global changes. We develop a protocol studying the resilience of the healthcare system at multiple levels in the context of climate change and variability, population mobility and the Covid-19 pandemic, both from an institutional and community perspective. METHODS: The conceptual framework designed is based on a combination of Levesque's Health Access Framework and the Foreign, Commonwealth and Development Office's Resilience Framework to address both outputs and the processes of resilience of healthcare systems. It uses a mixed-method sequential exploratory research design combining multi-sites and longitudinal approaches. Forty clusters spread over four sites will be studied to understand the importance of context, involving more than 40 healthcare service providers and 2000 households to be surveyed. We will collect primary data through questionnaires, in-depth and semi-structured interviews, focus groups and participatory filming. We will also use secondary data on environmental events sensitive to climate change and potential health risks, healthcare providers' functioning and organisation. Statistical analyses will include event-history analyses, development of composite indices, multilevel modelling and spatial analyses. DISCUSSION: This research will generate inter-disciplinary evidence and thus, through knowledge transfer activities, contribute to research on low and middle-income countries (LMIC) health systems and global changes and will better inform decision-makers and populations.