In this initial phase of conquest, most of the Georgian and Armenian nobles, who held military posts along the frontier regions submitted without any serious opposition or confined their resistance to their castles while others preferred to flee to safer areas.

Queen Rusudan had to evacuate Tbilisi for Kutaisi, leaving eastern Georgia in the hands of atabeg Avag Mkhargrdzeli and Egarslan Bakurtsikheli, who made peace with the Mongols and agreed to pay them tribute.

Although an Arabic chronicler Baybars al-Mansuri states that the Georgians took advantage of the Mongol invasion of Anatolia (1243) to seize the castles of Babrawan, Washlawan, and Bayburt.

By the mid-13th century, the Jaqelis realm thus incorporated most of the mountainous areas of north eastern Anatolia south of the Black Sea coast up to the edge of the plain of Erzurum.

Sargis I Jaqeli and David VII of Georgia "Ulu" rebelled against their Mongol overlords, a huge army of Mongols led by Arghun Noyan attacked the southern Georgian province of Samtskhe, defeated the king and his spasalar (general) Sargis Jaqeli, but could not capture the rebels’ main strongholds and left the country in June 1261.

In 1262, he had to make peace with the Mongols and returned to Tbilisi, effectively splitting the country into two parts with both rulers titled as kings of Georgia.

In 1265, the Georgian forces serving as a vanguard of the Ilkhanid army, defeated Berke, Khan of the Golden Horde, and expelled his troops from Shirvan.

Samtskhe managed to remain a culturally developed part of Georgia as well as maintaining territorial integrity, sometimes even expanding along its borders.

Despite being independent, Samtskhe still maintained some kind of relations with Georgia and Beka himself was given a title of Mandaturukhutsesi (Mandator) by Georgian king.

In 1334 George V of Georgia reasserted royal authority over the virtually independent principality of Samtskhe, ruled by his cousin Qvarqvare I Jaqeli.

In 1394, he dispatched four generals to the province of Samtskhe, with orders to apply the Islamic law of ghaza (i.e. the systematic raiding of non-Muslim lands).

[3] Timur nonetheless undertook some preventive measures and attacked the Georgian garrison of Tortumi, demolishing the citadel and looting the surrounding area.

Ivane Jaqeli, however, arrived with gifts, which offered Timur a good cause for keeping on reasonable terms with the rulers of Samtskhe.

With the decline of the Kara Koyunlu after Jahan Shah's defeat at the hands of Uzun Hasan in 1467, the Aq Qoyunlu became the major power in eastern Anatolia.

Kaikhosro with King Alexander I of Kakheti and Constantine of Kartli agreed to assist first Safavid shah Ismail to destroy Aq Koyunlu rule in Persia.

They made an alliance with the Georgian kings, Bagrat III of Imereti and Luarsab I of Kartli (c.1510–1565) to end up Jaqelian rule and protect Samtskhe from dominant Muslim empires (Ottomans and Safavids).

Qvarqvare died in prison, while Rostom was awarded his share of Samtskhe: Adjara and Lazeti, long sought after by the Gurieli dynasty.

A few years later, Qvarqvare's survived youngest son Kaikhosro II requested Ottomans to expel Imeretian and Kartlian forces from Samtskhe.