Food insecurity is prevalent in majority of Eastern African countries. In both Ethiopia and Rwanda, this is attributed to low agricultural productivity resulting mainly from high population density leading to land fragmentation and reduced land holdings; reliance on rain-fed agriculture; and continued intensive cultivation of land with no fallows and soil and water management strategies. The present studies conducted under the ‘Trees for Food Security Project’, aimed to characterize farming systems and elicit local knowledge on the role that trees and associated management play in increasing food security. This study was conducted between March-June, 2013, using AKT5 (Agro-ecological Knowledge Toolkit) software and methodology including semi-structured interviews, focus group discussions, transect walks and participatory resource mapping. Through stratified sampling, 94 stakeholders in Ejersa Jorro and Jawee Bofoo villages, East Shewa Zone, Ethiopia and 39 stakeholders from Rushubi, Bahimba and Nkomane villages in Gishwati, Rwanda were interviewed. In both study areas, tree retention on farms was mainly product and income-driven and less due to ecological services; with the overriding factors in East Shewa being dead fence, timber, fuelwood and farm and household tools; while in Gishwati were: fruits, climbing bean support poles, fodder, fuelwood and timber. This has resulted into frequent pruning that prevented tree regeneration and led to loss of trees’ ecological services such as soil erosion control, nutrient cycling and soil moisture regulation. In Gishwati, 30 species were encountered, 15 native and 15 exotic, with an average of 5 species per household; while in East Shewa, 40 species were encountered, with only 4 being exotic. Realizing the full potential of trees in achieving food security would require increasing tree species diversity and density in order to increase farmers’ resilience and benefits all year round. However, common factors limiting tree integration on farms in both study areas were: small land holdings and lack of tree germplasm. Other factors in East Shewa included livestock browsing, drought and farm mechanization; while in Gishwati were the farmers’ low knowledge on tree-crop interactions, utilities and ecological suitability. Therefore, in order to accelerate the adoption of trees, thereby contributing towards improved livelihoods, it is imperative to design interventions that tackle these challenges.