Afghanistan experienced an extraordinary situation in 2021, marked by intensified conflict, the Covid-19 pandemic, and prolonged drought. This article reflects on the research method and approaches employed to investigate these overlapping crises, and the applications of this approach to assess the livelihoods impacts of the pandemic in the context of conflict and climate change in Afghanistan. It relies primarily on field qualitative data collection and analysis from Kandahar and Herat provinces supported by further insights from the quantitative analysis of household survey data in 2019/20, part of which overlaps with the onset of the pandemic. Reflections on the methodology reveal the importance of longitudinal qualitative methods of analysis to understand the pathways through which layered crises can affect people’s lives and livelihoods. These research findings are used to develop implications for coherent development of policies and programming to better support poor and vulnerable Afghan people in the context of overlapping crises.