Habitat structure and complexity are two main components determining bird community diversity. Although a wide array of components contribute to the physiognomy of urban habitats, our knowledge of the habitat features that affect bird communities within urban areas is biased to vegetation. In this study, we measured 33 habitat characteristics that describe the spatial distribution of urban components, habitat structure, biological heterogeneity, potential hazards for birds, housing density, and socioeconomic level of three neotropical cities to define the relative role that vegetation and non-vegetation habitat features have on abundant, moderately abundant, and rare bird species. Our results show that bird species richness and abundances are positively related to vegetation cover and human prosperity, and negatively related to highly developed urban areas with intense human activities and high abundance of cats and dogs. We found six urban infrastructure variables related to bird species richness and abundances: (a) number of electric and telephone cables, lighting rods, and building height were positively related to abundant species, (b) electric and telephone poles and building cover were negatively related to moderately abundant species, and (c) lamp poles were negatively related to rare species, while electric and telephone poles were positively related. Our results revealed that abundant bird species were only related to urban infrastructure features (i.e., cables, lightning rods, building height), while moderately abundant and rare species were related to habitat structure and urban-related hazards, showing that life-history traits affect how species respond to urbanization. Based on our study, we suggest some urban management and planning policies, including: the increase of tree and shrub cover throughout cities, allowing shrubs and herbs to grow in areas restricted to pedestrians, controlling homeless dogs and restricting off-leash dogs, and considering the need of homogenizing the ecological quality throughout cities, regardless of socioeconomic boundaries.