(Lamyn Gegeen, Zayiin Gegeen and Shireet Gegeen - lamas recognized as a khubilgan, or reincarnation, and they were eventually given the title of the follows)

In ancient time, Lamyn Gegeen, Zayiin Gegeen and Shireet Gegeen decided that the base of the mountain would be a very auspicious place to build a monastery. But who should build this monastery and who should it be dedicated to?  Unable to decide, they placed their tea bowls in front of them. Whoever could first make a flower appearance in his bowl would have the honor of building the monastery. They closed their eyes and became to meditate. When they opened their eyes some time later a flower had appeared in the bowl in front of the Zayiin Gegeen. So they finally agreed that the Zayiin Gegeen should have the honor of building the monastery.

The monastery is located just in front of the huge granite massif known as Bulgan Uul. Nestled amongst forests of larch and white birch trees, the area is protected as a nature reserve and is home to deer, wild boar and birdlife. It has nine different parts, or peaks, each named after one of the Nine Precious Stones and Metals; gold; silver, bronze, pearl, coral, turquoise, brass, copper, and lapis lazuli.

The first temple of the new monastery—not including the temple built for the lama Sandui in 1631—was the Guden Temple, built according to local informants in the early 1680s. The Right, or Summer Semchin Temple, directly in front of the Guden Temple, was reportedly built in 1684, and the Left, or Winter Semchin Temple shortly thereafter. In 1710 the Tsogschin Dugan, which became the main temple of the monastery, was constructed.

 Luvsanperenlei, the First Zayiin Gegeen, apparently resided at Zayiin Khuree full-time after his return from Tibet. One of the outstanding scholars of his time, he wrote a massive history of India, Tibet, and Mongolia, among numerous other compositions. Luvsanperelei served as one of Zanabazar’s collaborators and teachers.  In 1715 the First Zaya Pandita died and his mummified body, sitting in the lotus position, was entombed in a stupa which was eventually placed in the Guden Sum. Many more temples and other buildings were constructed throughout the eighteenth and nineteenth centuries, and existing structures underwent extensive renovations, first in the 1880s and later in 1909-1910. The entire complex at one time must have covered a hundred or more acres, and by the 1920s Zaiyin Khuree was one of the largest and most influential monasteries in Mongolia, with over 2000 monks attached to eight different colleges. The monastery was also famous for its tsam dances, the last of which was held in July of 1932. Arkhangai Aimag, and particularly its monasteries were reportedly a hotbed of anti-revolutionary fervor, and Zayiin Khuree soon attracted the attention of the communist government. The Sixth Zaya Pandita was murdered by the communists in 1932 and eventually most of monastery, with the exception of the Guden Temple, the Semchin Temples, and the first temple built in 1631, was leveled. The Guden Temple was turned into a fire station and the 1631 temple was made into a small museum. Since the early 1990s the remaining portions of the monastery complex have undergone extensive renovations. The winter and Summer Semchins both now serve as well-appointed museums. In the Semchin Temple to the left, facing the main Guden Temple can be found the robes of the first Zaya Pandita, musical instruments used by musicians who entertained the various Panditas, and a host of other historical artifacts. In the left temple of the Guden Temple are the stupas containing the sharils, or mummified bodies of both the first and second Zaya Panditas, a portrait of the first Zaya Pandita painted in 1995 but said to be based on an original done in 1680, a portrait of Jambatseren, the sixth Zaya Pandita, and his wife or consort, an interesting tanka of the Tavan Khaan, or Five Kings and other items.

The middle temple of the Guden Temple also serves as a museum and includes a detailed scale model of the whole monastery as it existed before the 1930s. Just to the left of the walled compound containing the Semchin temples and the Guden Temple can be seen the ruins of the Tsogschin Dugan, once the main temple of the monastery.