BACKGROUND: Low- and middle-income countries (LMICs), including South Africa, are currently experiencing multiple epidemics: HIV and the rising burden of non-communicable diseases (NCDs), leading to different patterns of multimorbidity (the occurrence of two or more chronic conditions) than experienced in high income settings. These adversely affect health outcomes, increase patients' perceived burden of treatment, and impact the workload of self-management. This paper outlines the methods used in a qualitative study exploring burden of treatment among people living with HIV/NCD multimorbidity in South Africa. METHODS: We undertook a comparative qualitative study to examine the interaction between individuals' treatment burden (self-management workload) and their capacity to take on this workload, using the dual lenses of Burden of Treatment Theory (BoTT) and Cumulative Complexity Model (CuCoM) to aid conceptualisation of the data. We interviewed 30 people with multimorbidity and 16 carers in rural Eastern Cape and urban Cape Town between February-April 2021. Data was analysed through framework analysis. FINDINGS: This paper discusses the methodological procedures considered when conducting qualitative research among people with multimorbidity in low-income settings in South Africa. We highlight the decisions made when developing the research design, recruiting participants, and selecting field-sites. We also explore data analysis processes and reflect on the positionality of the research project and researchers. CONCLUSION: This paper illustrates the decision-making processes conducting this qualitative research and may be helpful in informing future research aiming to qualitatively investigate treatment burden among patients in LMICs.