The adoption of a systems approach to plant breeding, considering multiple global challenges together, is needed to make sustainable progress towards addressing these challenges. Trees have roles in countering many key planetary health concerns and this means they provide an excellent example of where a systems approach to plant breeding is needed, underpinned by their diversity in features, uses, users and production contexts, and by their multiple domestication pathways. Here, we provide evidence as to why adopting a systems approach to tree breeding is important in addressing global challenges and explain the features of the approach. We particularly consider the application of the approach, which in the case of trees we refer to as ‘tree diversity breeding’, at the forest–agriculture interface, using CIFORICRAF’s research for development work as a case study. We suggest measures that can be taken to support the adoption of the approach for tree genetic improvement.