While the literature on food deserts focuses on limited availability of food in urban settings, ‘food swamps’ may better characterize the extensive prevalence and accessibility of cheap, highly processed foods. For urban populations, access to nutritionally inadequate poor-quality food has dire developmental consequences. The long-wave impacts of malnutrition at gestational and early childhood stages are negative and can be non-reversible. Moreover, those who survive into adulthood may face a lifetime of sub-optimal physical and mental development that undermines the second and third UN Sustainable Development Goals—to end hunger and to ensure healthy lives. This paper assesses the long-term health vulnerability of children with limited access to adequate and nutritious food in rapidly urbanizing cities. The analysis focuses on the African Urban Food Security Network (AFSUN) data drawn from 6453 household surveys in 11 cities and nine countries in Southern Africa. The results indicate that children in these households are consuming a limited diversity of food, have limited access to resources and have greater odds of experiencing both short-term and long-term food and nutrition insecurity. These findings demonstrate an underlying vulnerability to long-term health impacts stemming from nutritionally inadequate diets, with potentially significant costs to human capital.