The fact that no Christian had a hand in the initial construction of this church is one of the many aspects that makes this church unique. According to legends, the king of Chempakasseri founded this shrine on an astrologer's suggestion to get relief from diabolic powers. Four Christian families were brought to Kudamaloor from nearby areas to worship and tend to the affairs of the church. While the old church is still preserved for its historical significance, a new and spacious church was constructed in 1971 to accommodate the growing number of parishioners.
The church gained prominence as a pilgrim centre since it is the home parish of St. Alphonsa, the first woman of Indian origin to be canonized as a saint. The Baptismal Font used for St. Alphonsa's baptism is still preserved here. 'Alphonsa Bhavan', the home where the Saint was born and brought up, has been converted into a pilgrim centre with a chapel on its premises.
St. Mary's Church has a unique oil painting of Jesus Christ that is believed to have been done 400 years ago. Jesus has been painted in sky blue colour here which makes the artwork quite distinctive. The rich history combined with the spiritual ambience makes St. Mary's Church one of the favoured destinations of devotees.