The Catholic diocese of Bathery was established in 1978 by Pope John Paul II and was formally inaugurated on 2 February 1979.

[1] In 1958 the Holy See extended the jurisdiction of the Eparchy of Tiruvalla further towards the North of Kerala and some districts of Karnataka and Tamil Nadu.

The Diamond Jubilee of the Malankara Reunion Movement was celebrated in the Eparchy on 20 and 21 September 1990 at Sulthan Bathery.

Wladislao Cardinal Rubin, the former Prefect of the Congregation for the Oriental Churches visited the Eparchy on 9 January 1981 and inaugurated the Pastoral Council and Parish Senate in the diocese.

On 18 December 1996 John Paul II appointed Varghese Ottathengil, the then Rector of St.Mary's Malankara Major Seminary, Trivandrum as the new Bishop of Bathery, He was consecrated as Bishop on 5 February 1997 at Mar Athanasios Nagar, Bathery by Cyril Mar Baselios.

He was appointed Apostolic Visitor for North America and Europe, and Auxiliary Bishop of the Archieparchy of Trivandrum, on 18 June 2001.

Isaac Mar Cleemis was consecrated as bishop on 15 August 2001 at St. Mary's Malankara Catholic Church, Thirumoolapuram, Thiruvalla.

Many parishes and mission stations, and social, charitable and educational institutions, were established to the Karnataka region of the Eparchy.

Joseph Mar Thomas was appointed as the third Bishop of the Eparchy of Bathery and enthroned on 13 April 2010.

As of 2013[update] the Eparchy of Bathery comprised the civil districts of Wayanad, Malapuram, Kozhikode, Kannur, Kasargode of Kerala State and Nilgiris of Tamil Nadu.

The ecclesiastical districts of the Eparchy were Bathery, Pulpally, Nilgiris, Nilambur, Edakkara, Kozhikode, Mananthavady and Kannur.