Indigenous and traditional foods crops (ITFCs) have multiple uses within society, and most notably have an important role to play in the attempt to diversify the food in order to enhance food and nutrition security. However, research suggests that the benefits and value of indigenous foods within the South African and the African context have not been fully understood and synthesized. Their potential value to the African food system could be enhanced if their benefits were explored more comprehensively. This synthesis presents a literature review relating to underutilized indigenous crop species and foods in Africa. It organizes the findings into four main contributions, nutritional, environmental, economic, and social-cultural, in line with key themes of a sustainable food system framework. It also goes on to unpack the benefits and challenges associated with ITFCs under these themes. A major obstacle is that people are not valuing indigenous foods and the potential benefit that can be derived from using them is thus neglected. Furthermore, knowledge is being lost from one generation to the next, with potentially dire implications for long-term sustainable food security. The results show the need to recognize and enable indigenous foods as a key resource in ensuring healthy food systems in the African continent.