Agroforestry landscapes in the Philippines provide benefits or ecosystem services that have traditionally and sustainably supported food production for rural communities and the protection of natural resources. However, the very continuity and sustainability of agroforestry is in question because of the rise of new generations of landscape users that can ascribe different values toward these benefits. Thus, this study highlights age-based local ecological knowledge (LEK) on these agroforestry-based ecosystem services to understand differences in the generational persistence and sources of their LEK. A structured survey was conducted with 36 youth, 36 middle-aged, and 36 elderly users of an agroforestry landscape in Libungan-Alamada Watershed in Mindanao, Philippines. This survey focused on the presence of LEK on seven provisioning and five regulating ecosystem services previously identified through multiple participatory exercises in the agroforestry landscape. Results indicated high LEK (more than 50% of knowledgeable respondents in all age groups) across all the ecosystem services, highlighting strong social-ecological interdependence on the agroforestry landscape. While generational persistence of local knowledge was observed, the knowledge sources varied depending on the age group or the ecosystem service. Intergenerational transfer of knowledge was prominent for provisioning ecosystem services. However, institution-based learning was essential for regulating services (e.g. climate change mitigation), especially for the youth. Experiential learning was the primary mode of knowledge acquisition for regulating services (e.g., biodiversity conservation) for the older generations. These results provide strong evidence to help guide policy actors, decision makers, and program managers as they promote, conserve, and restore agroforestry practices, especially in production-protection landscapes such as the Libungan-Alamada Watershed. The revised policy should be based on age-targeted interventions and proper learning entry points that have been found effective in this study.