Numerous bats use the troposphere for hunting, commuting, or migrating. High-altitude flying bats face various direct and indirect threats, including collision with tall anthropogenic structures and aerial vehicles, aerial fragmentation, reduced insect biomass, and the altered ambient conditions associated with climate change. Furthermore, dust and chemical pollutants in the troposphere might impair the health and survival of bats. Such indirect threats are diffuse regarding their origin and effect on bats, whereas direct threats are site and context specific. Overall, troposphere habitat conservation is hampered by the “Tragedy of the Commons” because its stewardship is in the hands of many. We conclude that high-altitude flying bats are likely to become more threatened in the near future because of the increased use of the troposphere by humans. Therefore, we should target the protection of the troposphere for organisms, such as high-altitude flying bats, that strongly depend on intact skies.