On his return from Rome he became the Vicar General (Proto Syncellus) of the Eparchy of Bathery. Pope John Paul II nominated Aboon Isaac Mar Cleemis as Apostolic Visitor and the Auxiliary Bishop of Trivandrum on 18 June 2001 for the Syro-Malankarites residing in North America and Europe. He was consecrated on 15 August 2001 at Tirumoolapuram, Tiruvalla, assuming the name Isaac Mar Cleemis.