The Southern African food system needs to be fixed. Climate change, hyperinflation, energy crises, conflicts and pandemics are widely implicated in the disarray. Several intervention strategies are provided in existing literature, including adopting or scaling up technological and institutional innovations. However, studies need to provide details on the nature of innovation and the technological innovations required. This gap in knowledge and literature has practical and policy implications. This article explores the innovation and transformation prospects of Southern African food systems using Botswana, Malawi and South Africa, selected based on their different stages of development. Underpinned by the food systems conceptual framework, this exploratory study used content analysis; the article identifies potential innovations and technological innovations usable in the food systems chain and explores opportunities and barriers for technological and institutional innovations in the purposefully selected countries. The study found several innovations and digital technological integration by different actors across the food system chain. It also identified the opportunities for and barriers to innovation. It concludes that innovation needs to be higher and requires the active role of national governments because they wield both the resources and political power to direct how resources can be used. Other countries in the sub-region can draw on the recommendations made in this study to inform their commitment to transforming their food systems.