In 1889 the Prefecture Apostolic of Assam was created and Shillong was a headquarter, it was entrusted to the German Salvatorian Fathers. With the outbreak of World War I, the German Salvatorian Fathers were forced to return to their country and the Jesuits of Calcutta looked after the Assam Prefecture till it was entrusted to the Salesians of Don Bosco in 1921.

In 1934, the Diocese of Shillong was erected and Rev. Louis Mathias SDB was appointed as the first Bishop of Shillong Diocese. In 1935 due to the transfer of Bishop Mathias to Madras, Bishop Stephen Ferrando SDB of Krishnagar Diocese was transferred to Shillong Diocese to replace Bishop Mathias and hence, become the second Bishop of Shillong.

In 1951 Dibrugarh Diocese was bifurcated from Shillong Diocese. In 1964 the Diocese of Shillong is being divided to new Diocese of Tezpur. In 1969 Shillong Diocese is raised to the status of a Metropolitan See and a new Ecclesiastical Province of Shillong-Guwahati was created and Most Rev. Hubert D’Rosario SDB was transferred from Dibrugarh to Shillong as the first Archbishop. The Archdiocese of Shillong-Guwahati was divided again in 1973 to form a Diocese of Tura. Next division of Shillong-Guwahati Archdiocese was the creation of Diphu Diocese in 1983. On 23rd September, 1990 Rev. Tarcisius Resto Phanrang SDB was appointed an Auxiliary Bishop of Shillong-Guwahati.Further bifurcation of Shillong-Guwahati Archdiocese was made in 1992 with the creation of Guwahati Diocese. On 30th August 1994 Archbishop Hubert D’Rosario went to his eternal reward. On 1st August 1995, Bishop Tarcisius Phanrang was appointed the Archbishop of Shillong. On 5th May 1999 Archbishop Resto Phanrang went to his eternal reward. At the death of Archbishop Tarcisius Resto Phanrang, Rev. Fr. Michael Marbañiang was appointed the Diocesan Administrator of the Archdiocese. On 2nd April 2000, Rev. Fr. Dominic Jala SDB was ordained Archbishop of Shillong Archdiocese.

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 new Bishops of Nongstoiñ and Jowai respectively. Thus the Archdiocese of Shillong was further bifurcated and the two new Dioceses were created. At present Shillong Archdiocese comprises of East Khasi Hills and Ri Bhoi districts of Meghalaya.