The Archdiocese of Verapoly, the mother diocese of all dioceses in Kerala was originally known as the Vicariate of Malabar. The Vicariate of Malabar has its origin in 1657, with the arrival of Carmelite Missionaries, most prominent among whom was Father Joseph of St. Mary, better known as Joseph Sebastiani. They had been deputed under Father Hyacinth as Apostolic Commissar, by Pope Alexander VII to effect a reconciliation of St. Thomas Christians of the Syro-Chaldaic Rite, who had seceded from their Archbishop Francis Garcia S.J. The majority of them had in 1653 revolted against the Archbishop and forsaking his authority by taking an oath for the purpose at the foot of a cross-thereafter called the “Coonen Cross” situated in Mattancherry, had made their own Archdeacon the Archbishop. By the efforts of Sebastiani, a large number of seceders were brought back to the true fold. Nevertheless, they refused to be under the authority of their lawful Archbishop or under any prelate of the Jesuit Order known as the “Paulists”.

Rome, being informed of the situation by Sebastiani in person, decided to entrust the Carmelites with the spiritual care of the Syro-Chaldaic Rite. For this purpose, the Vicariate of Malabar was erected by Pope Alexander VII on 3 December 1659. Sebastiani was consecrated Titular Bishop of Hierapolis on December 15, 1659, and sent back to Malabar, with the title of Vicar Apostolic and Administrator of the Archbishopric of Cranganore. The new Vicariate eventually established its headquarters in the island of Verapoly.

The conquest of Portuguese territories in Malabar and especially of Cochin in 1663 by the Dutch and the consequent expulsion of al Catholic Missionaries from the territories occupied by the Dutch and elsewhere, threatened the very existence of the Malabar Vicariate. Nevertheless, it survived under the Indian Prelate Parambil Chandy (Alexander de Campo) whom Sebastiani had consecrated as his successor before he left Malabar in 1663. Before long Carmelites were allowed to resume their ministration which was by then extended also to the Catholics of the Latin Church who were under Portuguese protection.