Although a growing number of studies address how Neotropical birds respond to anthropogenic disturbance and deforestation, we continue to poorly understand responses of groups of interacting species, such as mixed-species flocks in the Andes. In this study, we examined how attributes at landscape (i.e., percentage of forest cover within 1-km²) and local (i.e. structural complexity of microhabitat) scales shaped mixed-species flocks within five broadly-defined habitat types in the Northern and Central Andes. From 2007 to 2010, we systematically surveyed flocks along line transects in 97 1-km² plots distributed from Venezuela to Peru based on a stratified-random design. We recorded 220 avian species in 186 mixed-species flocks, with the greatest species richness and largest flocks detected in forested habitats. Understory insectivores were most closely associated with mature and secondary forests. Increasing forest cover promoted species richness and size of flocks, with particularly strong associations in successional habitats and shade coffee. Structural complexity was positively associated with flock size in early successional and silvopastoral habitats, where 20% increases in complexity doubled flock size. However, the opposite pattern was true in shade coffee and secondary forests. Encounter rates of flocks were poorly explained by simple metrics of forest cover and structural complexity. Unlike flocks reported in many lowland forests, Andean flocks tended to span all vertical strata, with fewer understory-specializing flocks (e.g. flocks led by Basileuterus warblers and Chlorospingus tanagers). Nonetheless, in such flocks, understory insectivores were most closely associated with mature and secondary forests. Our research supports the idea that managed habitats with overstory trees can contribute to flock conservation. Overall, our results further suggested that understory birds require the more forested of habitats (e.g., mature forest held almost twice as many understory specialists as other habitats), and may be less amenable to conservation with agroecosystems or working landscapes.