Agroforestry has attracted considerable attention in recent years because of its potential to reduce poverty, improve food security, reduce land degradation and mitigate climate change. However, progress in promoting agroforestry is held back because decision-makers lack reliable tools to accurately predict yields from tree-crop mixtures. Amongst the key challenges faced in developing such tools are the complexity of agroforestry, including interactions between various system components, and the large spatial domains and timescales over which trees and crops interact. A model that is flexible enough to simulate any agroforestry system globally should be able to address competition and complementarity above and below ground between trees and crops for light, water and nutrients. Most agroforestry practices produce multiple products including food, fiber and fuel, as well as income, shade and other ecosystem services, all of which need to be simulated for a comprehensive understanding of the overall system to emerge.