Most autism research has been conducted in high-income countries, with participants typically from White, upper-middle-income families. Given the disparities experienced by autistic individuals living in underserved communities globally, there is a critical need for research to include individuals from culturally, linguistically, socioeconomically, and geographically diverse backgrounds to understand their unique needs. Qualitative research has the potential to describe the “lived experience” of families historically underrepresented in the autism literature. Here we describe the logistical and methodological challenges of conducting focus group discussions with 22 caregivers of young autistic children living in Cape Town, South Africa. Logistical challenges included (1) recruitment, (2) response rate, and (3) resource access. Methodological challenges included (1) participant background and experiences, (2) interpersonal dynamics, and (3) research ethics. We present recommendations based on lessons learned to reduce these challenges and improve rigorous qualitative research practices in similar low-resource contexts. Lay abstract Most of the autism research to date has been conducted in high-income countries, with children and families typically from White, upper-middle-income backgrounds. However, we know there are significant inequalities that exist which influence how autistic individuals from diverse, underserved communities can access services they need. As many of these individuals have not been included in the majority of autism research to date, there is much we do not know about these individuals’ life experiences, which are critically needed to better inform the development and implementation of care for families from historically underrepresented groups. In this article, we describe the research process we took to conduct focus group discussions with 22 caregivers of young autistic children living in Cape Town, South Africa. We specifically describe the lessons we learned in implementing these focus groups and provide recommendations aimed at how to best reduce logistical and methodological challenges moving forward to improve research conducted in similar low-resource contexts.