Supporting the diversification of African agricultural systems by the further integration of nutritious, perennial ‘new and orphan crops’ (NOC) is seen as an important means to address malnutrition in Africa. The approach may be of particular relevance in the context of climate change, with the diversification of food systems possibly supporting more resilient food provision in the face of more variable weather patterns. Here, we relate how perennial NOC can support dietary diversity at a subnational level within a seasonal context based on crop portfolios. We also explore the resilience of the production of perennial crops, based on year-on-year crop yield data for eastern and southern African countries provided by the Food and Agriculture Organization Corporate Statistical Database (FAOSTAT). These analyses support the role of perennial NOC in creating resilient food systems and indicate a potential for compensatory annual–perennial crop combinations, although further research is needed on this point. Making use of FAOSTAT country-level trend data, we also relate constraints and potential opportunities for perennial food crop production. We then explain how NOC are currently being promoted in the region, with specific reference to the work of the African Orphan Crops Consortium and its breeder-training programme. We discuss the challenges faced in delivering perennial NOC planting material to farmers, which are exacerbated by climate change, and the measures that are being taken to overhaul delivery systems.