In 1984 Thomas became the vicar of St. Peter's Church, New Delhi, where he served for two years. In 1986 he left for Germany for higher studies and joined the Erlangen-Nuremberg University. After completing studies in German language, he moved to the Goettingen University in 1987 to pursue Syriac patristic studies. He returned to India in 1990, after being elected to the bishopric of the Outside Kerala diocese. On 3 January 1991, Thomas was ordained Mor Timotheos Thomas to assist the Metropolitan of the Outside Kerala diocese Mor Theophilos Thomas, who was getting old. On 12 January 1992 Theophilos Thomas died, and Mor Timotheos assumed full responsibility for the diocese.