Agroforestry research is being transformed from a collection of largely descriptive studies into more scientific approaches, based on process-oriented research. The development of agroforestry as a science should be based on four key features: competition, complexity, profitability and sustainability. Managing the competition between trees and crops for light, water and nutrients to the farmers’ benefit is the biophysical determinant of successful agroforestry systems. Simultaneous agroforestry systems are more susceptible to competition than sequential ones. A tree-crop interaction equation helps quantify competition vs. complementary effects on fertility. Alley cropping, a simultaneous agroforestry system, has limited applicability because the competition factor usually exceeds the beneficial fertility effects. The Faidherbia albida parkland, another simultaneous system, is almost always beneficial since the reverse phenology of F. albida minimizes competition while enhancing the fertility effect. Sequential systems such as relay intercropping and improved fallows also minimize competition but the processes responsible for crop yield increases are largely unquantified. New methodologies for reliably measuring complex below-ground interactions are being developed.