In the 16th century, the city came under the rule of the Ottoman Empire and became a sanjak centre in Çıldır Eyaleti.

In May 1918, the town and its district were occupied by the Ottoman army until their withdrawal by the Armistice of Mudros—the occupation resulted in the exodus of the local Armenian population which nearly perished due to starvation and disease.

[9] After the Russian takeover, most of the Muslim Georgians left the area for the Ottoman Empire, and in their place Christian Armenian refugees from Erzurum and Bayazid settled here.

The climate of Akhalkalaki is moderately humid with relative cold dry winters and long cool summers.

In April 2005, an agreement was signed to build a new railway connecting Turkey with Georgia and Azerbaijan, passing nearby Akhalkalaki.

The city was home to the Soviet-era 147th Motor Rifle Division (part of the 9th Army of the Transcaucasian Military District) up until the early 1990s.

[23] On September 19, 2020, a new basic combat training center was opened on the site of the former base in Akhalkalaki.