It was in 1889 that the Prefecture Apostolic of Assam was erected with Shillong as its headquarter and entrusted to the German Salvatorian Fathers for pastoral works. With the outbreak of World War I (1914-1918), the German Salvatorian Fathers were forced to return to their country and the Jesuits of Calcutta looked after the Assam Prefecture until it was entrusted to the Salesians of Don Bosco in 1921.

With the rapid growth and spread of the Church throughout the North Eastern region of India the Holy See decided to make the Assam Prefecture into a diocese. On 9 July 1934, the diocese of Shillong was erected and Rt. Rev. Louis Mathias S.D.B was appointed the first Bishop of Shillong with the responsibility of offering pastoral care for the whole North Eastern region.

On 1 April 1935 Bishop L. Mathias was transferred to Madras at the sudden death of Mgr. E. Mederlet S.D.B on 12 December 1934. On 9 June 1935, Mgr. E. Bars S.D.B was elected Vicar Capitular to guide the diocese until the appointment of a new Bishop in Shillong. In November 1935, Mgr. Stephen Ferrando S.D.B bishop of Krishnagar, was transferred to Shillong as its Bishop. He arrived in Shillong on 24 January 1936 to be the shepherd of this vast N.E region.

On 23 July 1951 Dibrugarh diocese was erected bifurcating the extensive diocese of Shillong. Again in 1964 Shillong diocese was further divided and the diocese of Tezpur was created. In 1969, Shillong diocese was raised to the status of a Metropolitan See and the Ecclesiastical Province of Guwahati-Shillong was created with Most Rev. Hubert D’ Rosario S.D.B as the Archbishop. Prior to his appointment to Shillong he was the Bishop of Dibrugarh. Shillong had as its suffragan sees the dioceses of Dibrugarh, Tezpur and Silchar. Subsequently the Archdiocese of Guwahati-Shillong was renamed as Shillong-Guwahati on account of the concentration of Catholics in the Shillong region.

The Archdiocese of Shillong-Guwahati was divided again in 1973 to establish the diocese of Tura. Another division of the Archdiocese took place with the creation of Diphu diocese in 1983. On 23 September 1990, Rev. Fr. Tarcisius Resto Phanrang S.D.B was appointed Auxiliary Bishop of Shillong-Guwahati. Again Shillong-Guwahati was further bifurcated and the diocese of Guwahati was created in 1992 with Bishop Thomas Menamparampil as the shepherd of the diocese.

On 30 August 1994 Archbishop Hubert D’ Rosario went to his eternal reward and Bp. Resto was elected Diocesan Administrator. On 1 August 1995 Bp. Tarcisius Resto Phanrang was appointed Archbishop of Shillong. On 5 May 1999 Archbishop Resto went to his eternal reward and at his death, Rev. Fr. Michael Marbaniang was elected Diocesan Administrator of the Archdiocese. On 2 April 2000 Rev. Fr. Dominic Jala S.D.B was ordained Archbishop of Shillong. Archbishop Dominic has chosen “to grow in the unity of the Holy Spirit” as the motto to guide him in his ministry as the shepherd of the Archdiocese.

The Archdiocese of Shillong was again bifurcated with the creation of the Dioceses of Jowai and Nongstoin. On 2 April 2006 Most Rev. Lopez Quintana, the Apostolic Nuncio to India, ordained Rev. Fr. Victor Lyngdoh and Rev. Fr. Vincent Kympat as the bishops of the newly created dioceses of Nongstoin and Jowai respectively. At present the Shillong archdiocese comprises of East Khasi Hills and Ri Bhoi districts of Meghalaya. On 10th October 2019 Archbishop Dominic Jala went to his eternal abode. Rev. Fr. John Madur was elected Diocesan Administrator from 2019 to 2021.

On 28th December 2020, Bishop Victor Lyngdoh the Bishop of Jowai was appointed the Archbishop of Shillong Archdiocese. He was installed on 6th February 2021 at the Cathedral of the Archdiocese. His motto is "With God all things are possible”.