Variation in bird community composition across habitats may be reflected by changes in species’ ecological characteristics. By their comparison between habitats, we can learn information about the factors underlying these changes. For this purpose, we used data from a nationwide breeding bird monitoring scheme surveying birds in 15 habitat types sorted into four broad categories (forests, open, urban, and humid habitats) in a central European country, Czechia. We considered life-history strategy, migration distance, climatic niche position, European rarity, and diet niche as species’ ecological characteristics and compared their mean values across the habitat types. Although habitat type explained a relatively low proportion of variability in these characteristics indicating that birds widely overlap in their habitat use, we observed significant differences in ecological characteristics between broad habitat categories, as well as between habitat types within a given category. For example, urban habitats hosted species with a generally lower degree of insectivory than forest habitats. Within forests, coniferous stands hosted species with colder climatic niches than deciduous stands. The greatest differences were observed among humid habitat types: species recorded in water bodies were rarer in Europe and had slower life-history strategies than species recorded in running water. Within the open habitat category, mining areas were the most specific habitat with long-migrating and warm-dwelling species. The observed patterns can be driven by various factors including habitat-specific selection pressures, biogeographic constraints, and human-induced habitat changes. On their basis, we discuss our findings.