Functional groups or guilds are now becoming popular in biodiversity conservation and monitoring as representative of the condition and status of a habitat as a whole. These can provide a rich source of additional evidence that can supplement evidence from studies based on taxonomic composition. In this study, we assessed differences in bird species and feeding guild assemblages across three habitat types within the Pantabangan-Carranglan Watershed and Forest Reserve (PCWFR), a major watershed in the Philippines located in the province of Nueva Ecija on central Luzon island. We sampled three habitat types during the wet and dry seasons from 2012–2016 using ground and canopy nets. After 4084 mist-net days, we captured 1191 bird individuals of 92 species and 41 families. Both species and feeding guild assemblages differed between habitats based on PERMANOVA (p = 0.001). Nineteen species and five feeding guilds differed in abundance between habitats. Our study demonstrated significant responses of the species and feeding guild assemblages of birds within the PCWFR to a disturbance gradient. We also found that feeding guild assemblage patterns were significantly correlated to species assemblage patterns. The use of guilds in bird monitoring can, thus, help facilitate the involvement of indigenous people and local communities, whose knowledge of birds is based on their observations of the environment, including traits that define these feeding guild classifications. However, there is potential to obscure the presence of taxonomically distinct lineages, such as the many endemic species and subspecies found on Luzon island and the Philippines. This concern is especially important in a megadiverse region like the Philippines. As such, we recommend the use of a functional approach in tandem with the traditional taxonomic approach in studying bird communities.