[1] His first assignments after ordination included Assistant Vicar of St. Mary’s Cathedral Basilica, Ernakulam, and then private secretary to Cardinal Joseph Parecattil.

Pope John Paul appointed him Bishop of Palghat on 11 November 1996 and he was installed there on 1 February 1997.

[1] He is recognized as an authority on inculturation, an opponent of globalization and violations of human rights, and an advocate for the need for the Church to be poor.

[3][4] His appointment, according to Cardinal Leonardo Sandri, Prefect of the Congregation for the Oriental Churches, reflected Vatican concern about the real estate transactions as well as "ecclesiastical division" among the clergy and the archieparchy's bishops.

[5] An installation service was scheduled for 23 June with Giambattista Diquattro, Papal Nuncio to India, and several other prelates in attendance, including Cardinal George Alencherry, whose authority as Major Archbishop of the Syro-Malabar Catholic Major Archeparchy of Ernakulam-Angamaly was suspended by Manathodath's appointment as administrator, completed his duty as apostolic administrator on 26/06/2019 .