The impacts of increased deforestation and overgrazing, exacerbated by a doubling of the human population since the early 1970s, has led to a noticeable decline in a number of the hotspot's species. Many steppe species, such as the Vulnerable great bustard (Otis tarda), have declined dramatically as a result of agricultural expansion and crop-improvement projects.

The greatest threat to the Turkish part of the Irano-Anatolian Hotspot is the development of irrigation schemes for agriculture and associated infrastructure, such as dams. For example, in the Konya Closed Basin, the excessive use of water for sugar-beet agriculture led to the loss of many large steppe areas and closed basin lakes. Lake Sevan in Armenia and the Javakheti mountain wetlands in Georgia are also largely destroyed. And in the Ararat Valley alone, some 1,500 square kilometers of swamps have been drained for agricultural development.

Other threats that have led to extensive loss of habitat in the hotspot, include overgrazing, overharvesting of woody plants for fuelwood, and mining. Military operations in Iraq, Iran and Turkey have also resulted in the loss of forests and wetlands. More than 90 percent of natural steppes in the region have disappeared, although the alpine meadows covering higher parts of the mountains area largely intact. In Iraq, only four percent of natural forests remain. The only pristine forested areas are on the inaccessible mountains of southeastern Turkey and in the neighboring territories of Iran. In total, no more than 15 percent of the original native vegetation of this habitat remains intact.