The Adoor Amalagiri Estate was acquired by His Grace Arch Bishop Benedict Mar Gregorios in 1965 July 24 from Mr. A. M. Joseph Anthraper. It was the dream of Mar Gregorios the integral development of the society through some educational establishments here. In 2010 the Diocese of Pathanamthitta was formed. This land became the property of Diocese of Pathanamthitta. In 2014 June Following the visionary steps of forefathers the first Bishop of Pathanamthitta His Excellency Yoohanon Mar Chrysostom started this College as the commencement of an educational hub in central Travancore.
Now Mar Chrysostom College is managed by the Malankara Catholic Higher Educational Society, Diocese of Pathanamthitta. Having a well-built legacy of inculcating knowledge, the Malankara Syrian Catholic Church has been carrying forward the vocation to educate younger generations, over the past eight decades. As a result, numerous eminent educational institutions par excellence in Kerala as well as India are run by this management. At present Mar Chrysostom College is proving itself as one of the perfect exemplars of the managerial dexterity of the Malankara Syrian Catholic Church.