From its peak of geographical extent, the church experienced a rapid period of decline starting in the 14th century, due in large part to outside influences. The Chinese Ming dynasty overthrew the Mongols (1368) and ejected Christians and other foreign influences from China, and many Mongols in Central Asia converted to Islam. The Muslim Turco-Mongol leader Timur (1336–1405) nearly eradicated the remaining Christians in the Middle East; thereafter, Nestorian Christianity remained largely confined to the indigenous communities in Upper Mesopotamia and the Malabar Coast of the Indian subcontinent.
The Church of the East was headed by the Patriarch of the East, an office that traces its origin to the Apostolic Age. The head of the church also bears the title "Catholicos". Like the churches from which it developed, the Church of the East has an ordained clergy divided into the three traditional orders of deacon, priest (or presbyter), and bishop. Also like other churches, it has an episcopal polity: organisation by dioceses, each headed by a bishop and made up of several individual parish communities overseen by priests. Dioceses are organised into provinces under the authority of a metropolitan bishop. The office of metropolitan bishop is an important one, and comes with additional duties and powers; canonically, only metropolitans can consecrate a patriarch. The Patriarch also has the charge of the Province of the Patriarch.
For most of its history the church had six or so Interior Provinces in its heartland in northern Mesopotamia, southeastern Anatolia, and northwestern Iran and an increasing number of Exterior Provinces elsewhere. Most of these latter were located farther afield within the territory of the Sasanian Empire (and later the Caliphate), but very early on, provinces formed beyond the empire's borders as well. By the 10th century, the church had between 20 and 30 metropolitan provinces According to John Foster, in the 9th century there were 25 metropolitans including in China and India. The Chinese provinces were lost in the 11th century, and in the subsequent centuries, other exterior provinces went into decline as well. However, in the 13th century, during the Mongol Empire, the church added two new metropolitan provinces in North China, Tangut and Katai and Ong.