Under his leadership, Georgia sent a large contingent to participate in the NATO-led ISAF mission in Afghanistan, launched several reforms to address the shortcomings of the war, and increased international cooperation in military education.

In March 1991, he was appointed as chief of staff to the 11th Battalion of Gori, a key armed formation in the midst of the First South Ossetian War, and kept that position through the coup d'état that overthrew President Gamsakhurdia.

[3] While war came to an end in South Ossetia in June, a new armed conflict began in Abkhazia in August that would last for more than a year, until the fall of Georgian forces at the hands of Russia-backed separatists in September 1993.

During the war, he led artillery forces in Tskhinvali and on the road leading to the Roki Tunnel, destroying several Russian columns of tanks coming to reinforce separatist positions.

After President Saakashvili ordered a major army reshuffle to address the shortcomings encountered during the war, Chankotadze was made Deputy Chief of the Joint Staff to replace Alexandre Osepaishvili, while Vakhtang Maisuradze took over as Artillery Brigade Commander.

[9] As the new commander-in-chief of Georgian forces, he had the task of reorganizing the military after the devastating Russo-Georgian war, while facing depleted resources and a decrease in international arms procurement.

[10] On May 5, 2009, a group of soldiers under the leadership of Lieutenant-General Mamuka Gorgiashvili mutinied at the Mukhrovani military base in what authorities would later describe as an attempt to disrupt NATO-led international exercises set to begin the day after.

[19] Chankotadze's term in office was characterized by Georgia joining NATO coalition forces in Afghanistan and sending a 173-strong company to fight under French command in Kabul's Camp Warehouse, mainly used to train the Afghan military.

The opposition to President Saakashvili routinely criticized Chankotadze's term for the perceived influence of Bacho Akhalaia, who was appointed as Minister of Defense in 2009 and was seen as the real decision-maker in armed forces decisions.

At the time, the Ministry of Defense and the State Service for Veterans Affairs condemned the statement, calling on armed forces and retired officers to not interfere in the electoral processes.

Around the same time, he also blasted the Ministry of Justice for making comments about the potential subpoena of active duty officers by the International Criminal Court over its war-related case.

In that race, he was at first considered as a potential nominee for the Parliament Majoritarian District of Tsqaltubo-Samtredia-Vani-Khoni, although UNM eventually nominated TV anchor Nanuka Zhorzholiani as a candidate, while Chankotadze appeared as 6th on the party's electoral list.

[24] During the campaign, the ruling Georgian Dream accused him of conspiring with MP Nika Melia and former UNM government official Dimitri Shashkini to lead provocateurs with "batons and electric shocks" ahead of the polls, allegations that have not been backed by evidence.

[29] Ahead of the 2021 local elections, he asked NATO Special Representative James Appathurai to ensure a "maximal presence" of foreign observers to watch the polls.