Despite the church's name, the church was actually found in regions that were part of the Russian Empire at the time of the founding. The church was originally found as the Eastern Church of the Yuan (Mongolian: Юанийн Зүүн Сүмийн) and later the Yuan Orthodox Church (Mongolian: Юань үнэн алдартны сүм), by descendants of Mongolic peoples converted to Russian Orthodoxy by Russian priests, as Russian rule began to weaken as well as the subsequent Mongolic and Siberian revolts against Russian rule, the Mongolic followers of the Russian Orthodox Church found their own section of the Eastern Orthodox Churches.
It was found by Michael Monkeev, also known as St. Michael of Sükhbaatar, an Orthodox monk from northern Mongolia, when it was under Russian rule.
Followers of the Mongolian Orthodox Church make up the majority of Christianity in Mongolia.
Unlike the Mongolians who follow the Tibetan Buddhist faith, the Mongolian Orthodox Christians continue to write the Mongolian language in the Cyrillic script. However, some of more culturally conservative Mongols within the church, such as the Oirats, are swaying away from Cyrillic, and adopting the native Uyghur-influenced Classical Script from their non-Orthodox counterparts, in an act of "pure Mongolness".
The Mongolian Orthodox Church was found simultaneously during the beginning of the Great Siberian-Mongol Revolt. In fact, it was one of the moves made by Mongol rebels, who were formerly Russian Orthodox, as a way of freeing themselves of Russian rule.
Mikhail Monkeyev (also Michael Möngkeyn) a former Russian Orthodox monk, left his original faith to go help his Mongolian brethren. In addition, Monkeyev had vengeful unfinished business with the Russian monarchs, due the kidnapping of his sisters to be used as housewives, concubines and even espoused to Russian princes.
Monkeyev also proclaimed descent from the emperors and rulers of the Yuan Dynasty, and Northern Yuan, and wanted to "restore" the legacy and prominence of the Chingissid dynasty. Monkeyev had even proclaimed that if Genghis Khan was a Christian, he would venerate him as a saint.
Monkeyev met with other former Mongolic Russian Orthodox leaders and clergy, to commence the Great Council of the Ten Monks (Mongolian: Арван Хуврагийн Их зөвлөл). It is this same council that waged an armed revolt against the Russian monarchs. As the new religious sect also attracted some Turkic and Siberian non-Mongol groups, and even recorded Chinese converts and followers, the new church was named the Great Eastern Church of the Yuan (Mongolian: Юанийн Зүүн Сүмийн, Chinese: 東元教會), according to Russian, Mongolian and Chinese records.
Monkeyev proclaimed himself the Patriarch of the Eastern Church of the Yuan. The Mongol rebels also recruited non-Orthodox Mongols, as they went forth to attack Russian military stations throughout Mongolian territory.
However, the Russian monarchs would later advance into Siberia, and defeat the rebels, initially ending the rebellion. However, Monkeyev fought to the last breath and last drop of blood, even as he was being cuffed and dragged by Imperial Russian soldiers to the execution area. He, along with seven other of the monks, were executed via firing squad.
Two of the other monks, Joseph Manduul and Alexander Jungdu, survived to keep the Mongolian Orthodox Church alive, through persecution as the Russian monarchs carried out persecutions and an attempted abolition of the church.
Joseph Manduul was then proclaimed as the Head Patriarch of the Eastern Church of the Yuan, and during this era the turn "Yuan Orthodox Church" (Mongolian: Юань үнэн алдартны сүм) was coined, by Russian and Chinese historians. Manduul venerated Mikhail Monkeyev, along with the seven executed monks as saints.
The Russian treatment of the Mongolian Orthodox community worsened, with the monarchy banning all Mongolic languages from use in churches and monasteries, banned Mongolic-language Bibles and ordered that all Mongols are instructed and educated in Church Slavonic and Russian in religious institutions.
In addition, the Russian monarchs sent princes and princesses to lead armies of officers to carry out inspections in Mongolic-speaking communities. Russian military presence was increased in Darkhan, Selenge and Ulaanbaatar.
Joseph Manduul commenced the Second Mongol Revolt, revolt that once-more, ended up in defeat. In addition, Manduul was killed in the battle against Queen Elena's forces, by Queen Elena herself.
Once more, the Mongolian Orthodox Church underwent persecution, many of the Mongolian Orthodox Christians fled to the mountains. Queen Elena tightened the Russian policy on the Mongolic-speaking Orthodox people even further, giving the Mongols the chance to either convert or revert to Russian Orthodoxy, or be killed. Those who refused to convert fled.
Alexander Jungdu was the only Mongolic Orthodox leader that remained alive. While fleeing, Jungdu already had plans for the third revolt. However, Queen Elena and Queen Alina pursued Alexander Jungdu. Jungdu's rebel forces fiercely fought the two queens' armies, at one point, was very successful in pushing the Russians back up north.
However, Elena and Alina, as well as their combined forces as well as Buryat collaborators, defeated Jungdu's forces.
Elena and Alina made a deal with Jungdu and the Mongolic Orthodox rebels, that if they surrender, end all of their revolts and help the Russians, the queens would attempt to lift the harsh policies against the Mongolic Orthodox communities.
Jungdu agreed to the deal. His followers rejoiced, and he then was proclaimed the Patriarch of the Mongolian Orthodox Church. The Treaty of Selenge was signed between the Mongolic chiefs and the Russian monarchs. This acknowledged Russian territorial autonomy over the Mongolic peoples, but also acknowledged the full religious freedom of the Yuan Orthodox Church. The treaty also bound the Mongolic people to aid the Russians in fighting threats, both external and internal.
Upon the signing of the treaty, Jungdu and the Mongolian Orthodox tribes held a memorial, honoring Monkeev and the eight other Mongolic Orthodox leaders, while also honoring their newfound friendship with the Russians.
During World War II, the invading Germans tried attempted to recruit Mongolian Orthodox to join them in their invasion of the Russian Empire and Soviet Russia. The Germans also promised the Mongols protection from the Chinese threat to the south.
Although agreeing at first, Head Patriarch Isaac Jamsrang relented, remembering the treaties made between St. Alexander and Queens Elena of Moscow and Alina of Kiev, ordering all the Mongols to unite not only amongst themselves, but along with the Russians to fight the German invasion. The united Mongolic peoples merged to form the Far-East Resistance Force (Mongolian: Алс-Дорнод эсэргүүцэл хүчин, Russian: Дальний Восток сила сопротивления), the Mongol and other native Siberian guerrillas and militants conducted raids against German formations. They also conducted surprised guerrilla attacks against German encampments at night, when nobody suspected an attack. Later, they helped the Imperial and Soviet Russian Forces in carrying out their offensives against the Germans.
Many Mongols joined Siberian sections and units of the Soviet Russian Forces, and engaged in offensives against the Japanese. One of the most successful was the Battles of Mongolia and Manchuria between the Russian Empire, Soviet Russia, Japanese Empire and the Socialist Democratic Republic of China where Mongols contributed 43% of the Imperial Russian forces, who ended up victorious against both the Japanese and Chinese forces.
Mongolian Orthodox preachers introduced the Mongolian Orthodox Church into Manchuria, which at that point, had become a trust-territory of Russia, in 1947. The first Mongolian Orthodox church was constructed in Jilin City that same year, and finished construction by 1948.
After Manchuria was officially declared an independent nation in 1952, many of the Mongolian Orthodox Christians, as well as other Mongols who took part in the Imperial Russian invasion, stayed in Manchuria, choosing to become citizens of the new nation and establish themselves there.
Nicholas Nergüi, the priest who ordered the construction of the Jilin church, became the Bishop of the Mongolian Orthodox Church in Manchuria. With the opening of a second church in Qiqihar, in the Mongolian-held portion of Manchuria up north, Nergüi became the Archbishop of the Mongolian Orthodox Church in Manchuria, and the Jilin church was turned into a Holy See.
At this time, Nergüi officially changed the name of the Yuan Orthodox Church to the Mongolian Orthodox Church, the name was officially used in 1953 and became the church's full legal name.
In the 1990s, many nationalist sections of the Mongolian Orthodox Church began attempts to further "Mongolize" the church, and purge it of Russian and Slavic influence. Solomon Jungsai, the Bishop of Jilin, attempted to abolish the use of Cyrillic and introduced the use of the Uyghur-descended Classical Mongolian script. Jungsai also hired linguists, scholars and translators to write, print and publish copies of the Bible in Classical Mongolian.
In 2011, the Holy Trinity Church in Ulaanbaatar, Mongolia, which long-stood as a Russian Orthodox Church, was converted into a Mongolian Orthodox Church and, and later a monastery. The current church is actually a rebuilt counterpart at the site of a Russian Orthodox Church of the same name, that was destroyed in 1948 by Japanese forces. The Holy Trinity Church is now under the jurisdiction of the Eparchy of Ulaanbaatar.