Indigenous knowledge has influenced native species selection in agroforestry systems worldwide. However, scientific advancements in plant sciences, agroforestry technologies and trade have accelerated species movements and establishment beyond their native range. Managing native and non-native species is an important area of research in agroforestry and this thematic issue includes 13 papers that cover a range of topics from the role of non-native species in agroforestry to management interventions to improve yield. As evident from these papers, non-native plants are still an important component of agroforestry in many parts of the world. Whether native or non-native, management interventions can increase the economic, environmental and social values of these species and that of agroforestry. Collectively, these papers attest to the increasing body of foundational knowledge in agroforestry.