A large body of evidence demonstrates the agronomic superiority of maize hybrids over open-pollinated varieties (OPVs) in intensive monoculture. However, comparisons of the performance of hybrids and OPVs in agroforestry systems are scarce. In this study, the performance of four maize hybrids and four OPVs is compared in sole crop and under mature trees. Experiments were conducted on-farm during four seasons in Bugesera, Rwanda and two seasons in Meki, Ethiopia. Two tree species were selected in Bugesera (Grevillea robusta and Senna spectabilis) and one in Meki (Acacia tortilis), and three farms were selected for each tree species, each including two plots with almost identical trees in their centre and two plots without tree. In Bugusera, grain yield was higher for hybrids (2 Mg ha−1) than for OPVs (1.5 Mg ha−1), and the presence of trees reduced the harvest index more in OPVs than in hybrids. In this region, the estimated reduction in grain yield due to the presence of trees was 0.9 and 1.1 Mg ha−1 in hybrids and OPVs, respectively, while estimated reduction in biomass was 1.5 and 1.7 Mg ha−1, respectively. In Meki, the grain yield of OPVs (2.08 Mg ha−1) and hybrids (2.04 Mg ha−1) did not differ and the presence of trees reduced their grain yields in the same manner. Our results showed that hybrids yielded more than OPVs under G. robusta and S. spectabilis in Bugesera but performed equally well under A. tortilis in Meki. We conclude that agroforestry farmers could benefit from growing hybrids in the equatorial savannahs of Rwanda, but that the choice between hybrid and OPV in equatorial savannahs of Ethiopia can simply be based on other factors such as seed costs and availability.