Hedgerow systems are widely adopted in the smallholder farms in the sloping grassland areas of Claveria, Mindanao, Philippines. The system is effective in addressing soil erosion problems and in conserving the topsoil. Gmelina arborea and Eucalyptus deglupta are two fast-growing timber species that are planted in hedgerow systems while maize is planted in the alley areas in between the hedgerows. Livestock holdings are widespread in Claveria, with 74% of the households having livestock. Cattle and carabao are the most common livestock in smallholder farms providing draught power for land preparation and transportation. In hedgerow systems, fodder tree leaves and crop residues are fed to livestock, while animal manure is added to the soil. Thus, these systems may serve as both a source and sink of methane and nitrogen oxides, depending on the management practices and component trees and crops of the system. This study aims to estimate methane emissions from livestock holdings and nitrogen oxide emissions through fertilization, tree litterfall and decomposition, maize residue incorporation and livestock manure from G. arborea and E. deglupta hedgerow systems