The second Mongol invasion of the Caucasus started with the expedition of Chormaqan against Jalal ad-Din Mingburnu, ordered by khan Ögedei in 1231. The Southern Persian dynasties in Fars and Kerman voluntarily submitted to the Mongols and agreed to pay tributes. To the west, Hamadan and the rest of Persia was secured by Chormaqan. The Mongols turned their attention to Armenia and Georgia in 1236. They completed the conquest of the Kingdom of Georgia in 1238 and the Mongol Empire began to attack the kingdom's southern possessions in Armenia, which was under the Seljuks the next year. In 1236 Ogedei despoiled Khorassan and populated Herat. The Mongol military governors mostly made their camp in Mughan plain. Realizing the danger of the Mongols, rulers of Mosul and Cilician Armenia submitted to the Great Khan. Chormaqan divided the Transcaucasia region into three districts based on military hierarchy. In Georgia, the population were temporarily divided into eight tumens. By 1237 the Mongol Empire had subjugated most of Persia, excluding Abbasid Iraq and Ismaili strongholds, and all of Afghanistan and Kashmir. The Mongols began conquering the North Caucasus in 1237, but encountered bloody resistance from the local populations there.
After the battle of Köse Dağ in 1243, the Mongols under Baiju occupied Anatolia, and the Seljuk Sultanate of Rûm and the Empire of Trebizond became vassals of the Mongols. Assassin strongholds lay scattered throughout Persia and the Caucasus, and Mongol commander Kitbuqa, under orders from Möngke Khan, began laying siege to them in 1253. Hulagu launched a full-scale assault in 1256 and eradicated Assassin presence from the region.
Following the destruction of Baghdad in 1258, civil war broke out between Berke Khan of the Golden Horde and Hulagu Khan of the Ilkhanate. Part of the larger Toluid Civil War succession conflict between Kubilai and Ariq Böke, the war consisted mainly of raids and invasions carried out by both sides throughout the Caucasus region, with Berke enlisting the aid of the Mamluk Sultanate and Hulagu the aid of the Byzantine Empire. Neither side gained a real advantage, and the conflict ceased after the victory of Kublai and his enthronement as Great Khan.
Mongol rule in the Caucasus lasted until the late 1330s. Greater Armenia stayed under Mongol lordship from 1220 to 1344. During that period, the King George V the Brilliant restored the kingdom of Georgia for a brief period before it finally disintegrated due to Timur's invasions of Georgia.
The Mongols made their first appearance in the Georgian possessions when this latter kingdom was still in its zenith, dominating most of the Caucasus. First contact occurred early in the fall of 1220 (Battle of Caucasus Mountain), when approximately 20,000 Mongols led by Subutai and Jebe pursued the ousted Shah Muhammad II of the Khwarazmian dynasty to the Caspian Sea. With the consent of Genghis Khan, the two Mongol generals proceeded west on a reconnaissance mission. They thrust into Armenia, then under the Georgian authority, and defeated some 60,000 Georgians and Armenians commanded by King George IV "Lasha" of Georgia and his atabek (tutor) and spasalar (commander-in-chief) Iwane Mkhargrdzeli at the Battle of Khunan on the Kotman River. George was severely wounded in the chest. The Mongol commanders, however, were unable to advance further into the Caucasus at that time due to the demands of the war against the Khwarezmian Empire, and turned back south to Hamadan. Once Khwarezmian resistance was all but mopped up, the Mongols returned in force in January 1221. Though King George was initially reluctant to give battle after his previous defeat, Jebe and Subutai forced him to take action by ravaging the countryside and killing his people. The ensuing battle at Bardav (Pardav; modern-day Barda, Azerbaijan) was another decisive Mongol victory, obliterating Georgia's field army. Though Georgia lay bare, the Mongols had come as a small reconnaissance and plundering expedition, not an army of conquest. Thus the Mongols marched to the north plundering northeastern Armenia and Shirvan en route. This took them through the Caucasus into Alania and the South Russian steppes where the Mongols routed the Rus’-Kipchak armies at the Battle of the Kalka River (1223).
These surprise attacks left the Georgians in confusion as to the identity of their attackers: the record of one contemporary chronicler indicates that he is unaware of the nature of the attackers and does not mention them by name. In 1223, when the Mongols had seemingly deferred their plans regarding Georgia, King George IV's sister and successor Queen Rusudan wrote in a letter to Pope Honorius III, that the Georgians had presumed the Mongols were Christians because they fought Muslims, but they had turned out to be pagans. The Mongol invasion also inadvertently altered the fate of the 5th Crusade. Georgia had planned to send its splendid army to open up a second front in the north at the same time as the European crusaders invaded from the west. Because the Mongols annihilated the Georgian army, it could not help, and the European Crusaders spent critical time waiting inactively for their allies who would never come.
During the invasion of Transoxania in 1219 Genghis Khan used a Chinese catapult unit in battle, they were used again in 1220 in Transoxania. The Chinese may have used the catapults to hurl gunpowder bombs, since they already had them by this time. In the 1239-1240 Mongol invasion of the North Caucasus, Chinese weapons were once again used.