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The COVID-19 pandemic has had wide-ranging implications on the academic community and there have been numerous commentaries on the effects of the pandemic on qualitative health research. However, the vulnerabilities faced by participants and researchers during the pandemic have remained underexplored. Addressing this gap, this reflective article discusses the intersecting challenges and opportunities arising for participants and researchers in qualitative health research during the pandemic through the lens of layered vulnerability. Vulnerability, as a layered concept, provides novel insight to discussions on the effects of the pandemic as it provides a depth of insight into the multifaceted and dynamic nature of vulnerabilities, while considering individual differences and contexts. Reflecting on the research we conducted during the pandemic, we draw out the layers of vulnerability that both participants and researchers faced during the research process, as well as the obligations and strategies we developed to mitigate these vulnerabilities. We discuss the intersectionality of individual characteristics and the digitisation of work and life, including the impact of moving qualitative health research online and the use of creative methodological approaches. Our article highlights how, through engaging with their own vulnerabilities throughout the research process, researchers can develop creative and new solutions for qualitative research which mitigate the increased vulnerabilities participants faced during the pandemic.