This paper explores the disproportionate impact of COVID-19 on internal migrants in the urban centres of Cape Town and Johannesburg, South Africa. Focusing on the socio-economic and livelihood challenges faced by this population, the research utilizes a survey conducted in 2023 to investigate how the pandemic exacerbated existing vulnerabilities. Results highlight significant disruptions in employment, increased economic hardship, and heightened health risks among migrants, particularly those living in low-income neighbourhoods. Despite the hardships, very few migrants intended to permanently return to their rural origins, indicating a complex interplay between economic necessity and pandemic-induced constraints. The findings underscore the unique challenges faced by internal migrants during health crises and suggest the need for targeted policy interventions to address the specific needs of this group within urban pandemic responses.