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.