The monastery is located in front of the huge granite massif known as Bulgan Uul. It was built in forest of larch and white birch tree. The area is protected as a nature reserve and is home of deer, wild boar and bird. It has nine different 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 was the Guden Temple was built according to local informants in the early 1680s. The Right Summer Semchin Temple, directly in front of the Guden Temple, was reportedly built in 1684 and the Left 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 lived at Zayiin Khuree full-time after he returned 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 temple. Many more temples and other buildings were constructed throughout the eighteenth and nineteenth centuries and existing structures underwent extensive renovations in the 1880s and in 1909-1910. Once in the past, the entire complex covered more than hundred acres and by the 1920s, Zaiyin Khuree was one of the largest and most influential monasteries in Mongolia, with over 2000 and eight different Buddhist colleges. The monastery was also famous for its Tsam dance, religious dance that was held in July of 1932.

Arkhangai province 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 mummified bodies of both the first and second Zaya Panditas, a portrait of the first Zaya Pandita painted in 1995 but it is 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. In the left of the walled compound, Semchin temples and the Guden Temple can be seen the ruins of the Tsogschin Dugan, once the main temple of the monastery.