One of the greatest threats to biodiversity is land use change. Habitat alteration can have strong impacts on functional diversity, i.e., the range of biological traits within a suite of organisms. Mixed species avian flocks are integral to maintaining both taxonomic and functional diversity in tropical forests as they provide participants with greater foraging efficiency, reduced predation risks, and increased resiliency of species and ecosystems to environmental change. Our aim for this study was to determine the effects of land use change on the taxonomic and functional structures of mixed species avian flocks in and around Cajas National Park, Azuay Province in the tropical Andes of southern Ecuador by comparing non-native vegetation in agricultural plots and forest regenerating from historical use as pastureland to the largest intact primary forest in the region. We found no changes in species richness and diversity or functional richness of flocks across habitats, but we did find significant differences in species composition. Surprisingly, we found higher functional diversity and uniqueness of flocks in regenerating forest with more diverse and structurally complex vegetation, but native and non-native forests were functionally similar. We did, however, find significant differences in the community weighted means of four of five functional traits in different habitat types. Overall, the taxonomic and functional structures of mixed species flocks in this region seem relatively unaffected by land use change, indicating flocking as a beneficial strategy for species with higher sensitivities to disturbance in areas with anthropogenic activities. It is critical to maintain functional diversity in ecosystems, as a greater variety of functional traits and functional redundancy implies an efficient and more resilient ecosystem in the face of environmental change. Mixed species flocks provide membership benefits that may mitigate impacts of disturbance via land use change and thus can be considered essential units for conserving avian biodiversity.