The impact of agroforestry on food security of upland farmers is least recognized and appreciated given that the linkage between them is quite complex and not well understood. The crucial role of agroforestry in enhancing food supply and augmenting family income is commonly ignored. This study aimed to get a deeper understanding of the role of agroforestry in ensuring food security of farming households in the Philippine uplands. A combination of participatory approaches including participatory rural appraisal, household survey, focused group discussions, field experiments and simulation modeling were used for the study conducted in Claveria, Northern Mindanao, Philippines. The first major finding was that the prime responsibility for ensuring adequacy of food production and supply for the farming households rested on the husband and wife. The second major finding based on the simulation results was that agroforestry increased and stabilized corn yields under hedgerow system. Moreover, fruits from perennial crops and trees served as secondary food crops especially during lean months of food supply. The last major finding was that the adoption of agroforestry significantly increased the level of benefits by around 42–137%, compared with the low income from continuous annual monocropping. The key to making upland farm households food secure is to increase the productivity of their farms and home gardens. A good start is to promote the agroforestry system in upland areas, and it is thereby recommended that both national and local government units mainstream their policies and efforts toward promotion of agroforestry adoption in the Philippine uplands.