The chapel is the heart of the campus which outpours the heavenly bliss through the continuous incensing and prayers by the holy Church. The chapel is dedicated in the honor of the St. Thomas, the Holy Apostle of India. The seven canonical-hour prayers in the chapel create a reverberation in the atmosphere of the seminary which spreads its rays to the calm and serene surroundings. This chapel has witnessed a continuous chain of many historical events from the time of the influence of western missionaries till today. The chapel is in fact the spiritual nurturing point of many generations that passed. It has been an abode for many who seek a peaceful shelter in Christ.
The canonical prayers in the chapel is a unique experience for the partakers of worship, with united and well disciplined liturgical arrangements, songs, readings and prostration. The prayers in the Seminary Chapel follow the standard Orthodox pattern with the daily cycle commencing with the Ramsho (Evening Prayers) at 6pm. Compline is said at 9.30pm. Lillyo (Night) and Sapro (Morning) are conducted from 5am onwards. Noon prayers are said at 12.30pm. The Seminary community celebrates Holy Communion every Wednesday at 7am as a “Community Qurbana” with the liturgy being celebrated by Faculty members. Devotional talks are conducted every Wednesdays following the evening prayers. Holy Liturgy is also every Sunday (morning prayers at 7am and Qurbana at 8am) and on all feast days in which a large number of faithful participate. The ambience not created but natural, attracts pilgrims to this Holy place.
The holy relics of founder Late Joseph Mar Dionysius II (Pulikkottil I), Joseph Mar Dionysius V (Pulikkottil II), St. Geevarghese Mar Dionysius (Mar Dionysius VI) and Paulose Mar Gregorios are buried in the chapel. The wall of Holy Sanctuary is decorated with the mural paintings with natural colours. The Holy Cross and icon of Christ is mounted at the top of the beskudishin for veneration. The cherubims guard the symbolism of the tabernacle. The lighted candles, the elevated Holy Gospel and the other symbolic ornamentations add to the heavenly impression.