This study surveyed Egypt's key regions, the Nile Valley and Delta, the Western Desert, the Eastern Desert, and the Sinai Peninsula. The 2020–2023 survey was focus on bat and bird reproductive and foraging areas. The study also records keystone species, particularly apex predators. Avian species, known as natural pest controllers, are being assessed to determine if their population has fallen or remained steady and to determine the causes. Egypt has 20 bat species and 501 bird species that naturally control pests. Rousettus aegyptiacus, Rhinopoma microphyllum, Rhinopoma cystops, Asellia tridens, Taphozous perforates, Taphozous nudiventris, Pipistrellus kuhlii, and Plecotus christii were identified from Egyptian bat and bird species. Pharaoh Eagle Owl (Bubo ascalaphus), Little Owl (Athene noctua), Barn Owl (Tyto alba), Yellow-billed Kite (Milvus migrans Aegyptius), Black-Winged Kite (Elanus Caeuleus), Cattle Egret (Bubulcus ibis), and Common Kestrel (Falco tinnunculus) are also important bird species that reproduce in these areas. This invasive species kills all young and eats eggs, preventing them from performing vital ecosystem services. Since bats are coronavirus reservoirs, the continuous coronavirus campaign in Egypt between 2018 and 2022 eliminated more than ten R. aegyptiacus colonies. Bats and birds have little effect on humans, hence do not justify unjustifiable punishment. It must strictly follow Law 4/1994 (amended by Law 9/2009), which protects all Egyptian bats and birds. It needs government and non-government cooperation to control exotic bird species like the House Crow and Common Mayna.