The COVID-19 pandemic heightened awareness that serious illness and injury are common and important shocks that result in food insecurity, the loss of livelihoods, and unsustainable coping strategies. These have significant negative impacts on welfare, especially for the poorest, driving up health care expenditure, reducing capabilities for productive and reproductive activities, and decreasing capacity to manage climate and other changes. These negative impacts are especially pertinent for countries in Africa where the high prevalence of communicable diseases such as HIV/AIDS and malaria have resulted in repeated health shocks. Unusually, the prevalence of these illnesses results in their impact being similar to those of covariate shocks, increasing the risk of poverty for entire communities and reducing options for coping strategies. Livelihood disruptions arising from the COVID-19 pandemic may have similar consequences for African food systems. The pandemic is likely to exacerbate existing dynamics of risk and introduce new and unanticipated changes to food systems. Although the initial focus of governments has been on public health interventions, preserving and growing resilient food systems is critical if livelihoods are to be protected. This paper discusses the implications of these evolving forms of risk and uncertainty for sustainable African food systems, reflecting on lessons from other systemic shocks.