Eparchy of Kottayam was erected exclusively for southist (Knanaya) Catholics in 1911. Knanaya Community tracks its origin to a group of Jewish-Christian emigrants from Southern Mesopotamia to the Southern India port of Cranganore in AD 345, who remains an endogamous community till date. They co-exited with the native St. Thomas Christians in India and embarked on a mission to re-invigorate the Church to St. Thomas. The first migrants consisted of about 400 people from 72 families of 7 steps headed by Thomas of Knayi. A bishop by name Uraha Mar Yousef, four priests and several deacons from part of the group.

Exactly as the Catholics of East had promised the emigrants, that he would send bishops to India, from time to time, Uraha Mar Yousef always had successors till the end of 16th century. Under the patronage of East Syrian Bishops, Knanaya Community had their own separate parishes and priest. This system continued even under Latin Rite European bishops, who governed the St. Thomas Christians later. When ritual Catholics, in 1887, all Knanaya Catholics, de facto, fell under the Apostolic Vicariate of Kottayam. Holy See asked Bishop Charles Lavige to appoint a separate Vicar General for Knanaya Community. As Vicariate Apostolic were re-organized into Trichur, Ernakulam and Changanassery and three indigenous bishops wre appointed for Syro- Malabarians in 1896, the bishop nominated for the Vicariate of Changanassery was Mar Mathew Makil, former Vicar General for Knanaya Community.

On August 29, 1911, a new Vicariate Apostolic of Kottayam was erected solely for Knanaya Community by the Apostolic letter “In Universi Christiani” by His Holiness Pope St. Pius X. On December 21, 1923, Vicariate Apostolic of Kottayam was raised to an Eparchy by Pope Pius XI. When territorial limits of Syro-Malabar Church was extended in 1955, jurisdiction of Eparchy of Kottayam was made co-extensive with the then extended territory of the Syro-Malabar Church. 

On December 23, 2003, His Holiness Pope John Paul II made a sovereign promulgation (Pro Gente Suddistica) that the Satus quo of Eparchy of Kottayam must be retained and he left it to the Bishops’ Synod of Syro-Malabar Church to decide on the desired enhancement of the juridical status of the Eparchy of Kottayam. I November 2004, the Synod gave consent to elevate Eparchy of Kottayam to the rank of a Metropolitan see without a Suffragan Eparchy. On March 21, 2005, Congregation for Oriental Churches issued a letter of no-objection to the decision of the Bishop’s Synod. Accordingly, on May 9, 2005, Major Archbishop Mar Varkey Cardinal Vithayathil issued the decree “The Eparchy of Kottayam” elevating Eparchy of Kottayam to the rank of a Metropolitan See. Through another decree, “God our loving father”, he appointed Metropolitan see of Kottayam. On June 3, 2005, feast of the Most Sacred Heart of Jesus, at aliturgical service, Major Archbishop canonically erected the Metropolitan See of Kottayam, ordained and enthroned Mar Kuriakose Kunnacherry, first Metropolitan of Kottayam. Mar Mathew Moolakkatt ascended as Metropolitan of the Archdiocese of Kottayam on 14 January, 2006.