While journeying home, they stayed in Goa where Kariattil died before he could formally take charge. Before he died, Kariattil appointed Kathanar as the Administrator of Kodungalloor Archdiocese after him. The new administrator ran the affairs of the church, establishing his headquarters at Angamaly. In 1790, the headquarters of the Archdiocese was shifted to Vadayar, dodging the invasion of Tippu Sultan. In the last four years of his life, Thomma Kathanar managed church administration from his own parish, Ramapuram.
