BackgroundIndigenous knowledge and responses were implemented during the COVID-19 pandemic to protect health, showcasing how Indigenous communities participation in health systems could be a pathway to increase resilience to emergent hazards like climate change. This study aimed to inform efforts to enhance climate change resilience in a health context by: (1) examining if and how adaptation to climate change is taking place within health systems in the Peruvian Amazon, (2) understanding how Indigenous communities and leaders’ responses to climatic hazards are being articulated within the official health system and (3) to provide recommendations to increase the climate change resilience of Amazon health systems.MethodsThis study was conducted among two Peruvian Amazon healthcare networks in Junin and Loreto regions. A mixed methodology design was performed using a cross-sectional survey (13 healthcare facilities), semistructured interviews (27 official health system participants and 17 Indigenous participants) and two in-person workshops to validate and select key priorities (32 participants). We used a climate-resilient health system framework linked to the WHO health systems building blocks.ResultsIndigenous and official health systems in the Peruvian Amazon are adapting to climate change. Indigenous responses included the use of Indigenous knowledge on weather variability, vegetal medicine to manage health risks and networks to share food and resources. Official health responses included strategies for climate change and response platforms that acted mainly after the occurrence of climate hazards. Key pathways to articulate Indigenous and official health systems encompass incorporating Indigenous representations in climate and health governance, training the health work force, improving service delivery and access, strengthening the evidence to support Indigenous responses and increasing the budget for climate emergency responses.ConclusionsKey resilience pathways call for a broader paradigm shift in health systems that recognises Indigenous resilience as valuable for health adaptation, moves towards a more participatory health system and broadens the vision of health as a dimension inherently tied to the environment.