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Objectives: The COVID-19 pandemic impacted food systems, health systems and the environment globally, with potentially greater negative effects in many lower-middle income countries (LMICs) including Indonesia. The purpose of this qualitative study was to investigate the potential impacts of the COVID-19 pandemic on diets, health and the marine environment in Indonesia, based on the perspectives of a multidisciplinary group of informants. Methods: We conducted remote in-depth interviews with 27 key informants from many regions of Indonesia, who are either healthcare providers, nutrition researchers or environmental researchers. Interview question guides were developed based on a socio-ecological framework. We analyzed the data using a qualitative content analysis approach. Results: Informants suggested that while the COVID-19 brought increased awareness about and adherence to good nutrition and health behaviors, the impact was transitory. Informants indicated that healthy food options became less affordable, due to job losses and reduced income, suggesting a likely increase in food insecurity and obesity. Environmental researchers described higher levels of marine pollution from increase in hygienic wastes as well as from plastic packaging from food orders. Conclusions: Our findings reveal perceptions by informants that the increased awareness and adherence to health behaviors observed during the pandemic was not sustained. Our results also suggest that the pandemic may have exacerbated the double-burden paradox and marine pollution in Indonesia. This study offers information for generating hypotheses for quantitative studies to corroborate our findings and inform policies and programs to mitigate the long-term impacts of the COVID-19 on diets, health, and the marine environment in Indonesia.