This church was established in CE 1225 in the name of St. Thomas. The church was established by Kunnathery Kunchako Tharakan, who was minister to the Ruler of Vadakkankoor (Kaduthuruthy), when Villarvattom Swaroopam still existed.
The paintings and sculptures in Mulanthuruthy Church Madhaba are world famous. The row of angels on the pillars of the Rathal, which has intricate carvings on them, is something unseen elsewhere. The depiction of Adam and Eve before eating the forbidden fruit from the tree of knowledge is one of the best creations in sculpture. The scene of the Last Supper, where Judas is sitting with a purse full of silver coins, St. Peter is holding aloft the key to heaven, Christ is raising the chalice while looking harshly at Judas, and John is lying on the lap of Jesus while leaning his left hand on to His body, is considered to be a blend of facts and symbolism, more than an appeal to emotions.
The upper layer depicts the wonders performed by St. Thomas in Kerala. One of them shows St. Thomas retrieving a huge log from the sea using a string. The poignant depictions of King Herod presenting the head of John the Baptist to the dancer Salome, on a silver plate, the figure of Virgin Mary holding baby Jesus, the scene of the resurrection of Christ, are all preserved in its original form, at the St. Thomas Church, Mulanthuruthy.