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Abstract Background By 2022, the Government of Indonesia had successfully eliminated malaria in 389 out of 514 districts but continues to face a challenge in Eastern Indonesia where 95% of the total 2021 malaria cases were reported from Papua, West Papua and Nusa Tenggara Timur provinces. There is an increased recognition that malaria elimination will require a better understanding of the human behavioural factors hindering malaria prevention and treatment, informed by local context and local practice. Methods This research used a light-touch immersion research approach. Field researchers lived in communities over several days to gather data through informal conversations, group-based discussions using visual tools, participant observation and direct experience. The study was conducted in four high malaria endemic areas in Papua, West Papua, and Sumba Islands in Nusa Tenggara Timur. Results The research highlights how people’s perception of malaria has changed since the introduction of effective treatment which, in turn, has contributed to a casual attitude towards early testing and adherence to malaria treatment. It also confirms that people rarely accept there is a link between mosquitoes and malaria based on their experience but nevertheless take precautions against the annoyance of mosquitoes. There is widespread recognition that babies and small children, elderly and incomers are more likely to be seriously affected by malaria and separately, more troubled by mosquitoes than indigenous adult populations. This is primarily explained by acclimatization and strong immune systems among the latter. Conclusions Using immersion research enabled behaviour research within a naturalistic setting, which in turn enabled experiential-led analysis of findings and revealed previously unrecognized insights into attitudes towards malaria in Eastern Indonesia. The research provides explanations of people’s lack of motivation to consistently use bed nets, seek early diagnosis or complete courses of treatment. The felt concern for the wellbeing of vulnerable populations highlighted during light touch immersion provides an entry point for future social behaviour change communication interventions. Rather than trying to explain transmission to people who deny this connection, the research concludes that it may be better to focus separately on the two problems of malaria and mosquitoes (especially for vulnerable groups) thereby resonating with local people’s own experience and felt concerns.