Better integrating currently under-researched nutrient-rich new and orphan crops (NOC) into food systems could play an important role in addressing poor human diets. Understanding the multiple interventions required to support effective integration is, however, not straightforward. Current research to support this objective has generally been inadequate, in large part because insufficient attention has been given to draw together the multiple disciplines needed to explore and reach solutions. A broad interdisciplinary research programme is needed to provide answers to the following questions: how do dietary diversity and crop diversity interrelate at national and local food system levels? What drives crop integration or exclusion in food systems over time? How can new technologies be embraced in combination with best existing practices to genetically improve, better manage and more effectively process crops? And what are the best approaches to bring about behavioural change among farmers, food processors, consumers and other stakeholders to introduce new practices and foods?These questions are of particular pertinence in sub-Saharan Africa (SSA) where the problem of ‘hidden hunger’ is especially significant. Specific initiatives such as the African Orphan Crops Consortium (AOCC), which seeks to apply new technologies to genetically improve 1-1nutritionally-important annual and perennial NOC in the region to help address hidden hunger, have to be viewed within a food system context if they are to be effective. Here, we explore food system issues affecting the SSA region, consider the specific crops and interventions of the AOCC initiative, and draw out six possible ‘quick win’ knowledge generating activities that, if undertaken, will support AOCC objectives and NOC integration. Through setting out research needs, our intention is to promote the creation of broad interdisciplinary teams to carry out systems-oriented work on NOC. We also hope to encourage other stakeholders, including funding agencies, to support this important research, in SSA and elsewhere.