Tibet groaned under the separation that began in the mid-9th century. This situation continued for 400 years and ended in the mid-13th century, when the religious circle headed by the Sagya Sect of Tibetan Buddhism pledged allegiance to the Yuan Dynasty. From then on, Tibet became a part of Chinese territory. The Sagya regime was headquartered in Sagya, the Pagmo Zhuba regime in Nedong of Shannan, and the Tsangpa Desi regime in Xigaze. Lhasa was not again the center of power in Tibet for 800 years, but remains to be the oldest holy city of the region.

After some 100 years, Tibetan Buddhism revived in the late 9th century and the early 10th century. Monastic rules spread from the Guge Kingdom in Ngari and Dandi in Qinghai to U-Tsang. As a result, Lhasa and its surrounding area again saw the flourishing of Buddhism. In Tibetan history, this is known as the "Revival of Tibetan Buddhism." For a prolonged period of time thereafter, Lhasa was under the rule by Tsapa wan hu (10,000-household) office. Office heads won the official title of situ from the Yuan court and were put in charge of Lhasa and the Lhasa River Valley. They exercised effective management over Lhasa and organized efforts to reinforce river dams, dredge water ways, build civilian housing, renovate the Barkor Street, repair the Jokhang and Ramoche Monasteries, protect buildings on the Potala Palace Ruins, manage various monasteries and Buddhist activities, organize lectures on Buddhist doctrines, build the Tantric School, compile history books, and publish books on Buddhism. People of later generations erected the statue of Lhagyi Gowaboin, one of the wan hu (10,000-household) office heads, in the Jokhang Monastery to honor what he had done for the city.

Buddhism boomed in Lhasa during that period. Monasteries built included the Sangpo, Jormolung, Gedong, Curpu, Chigung, Daglung, and Zho Monasteries. Although these monasteries were all built in areas around Lhasa, Lhasa remained the mecca for Buddhists.