The temple, dating back to the eleventh century, is associated with the Kottayam Raajas, who were devout followers and held special privileges at the Kottiyoor temple. The ritual of offering prasaadam to the Kottayam Raaja by the temple priest was conducted in a unique manner. According to the tradition, the Raaja, after receiving the prasaadam in a silver bowl, would place the bowl back at the same spot. However, there was an incident where a child from the Royal family took the bowl from the Raaja and refused to return it to the priest. Since the Royal family was responsible for the temple's maintenance, the more priest did not insist on reclaiming the bowl and allowed the child to keep it. When the Raaja insisted that the child return the bowl, the child still refused. As the bowl belonged to the temple, this caused concern for the Raaja. Consequently, he conducted a prashnam, a ritual for seeking divine guidance, at his palace. The prashnam revealed the significance of Kottiyoor as a sacred sacrificial site and emphasized that no one should take any article belonging to the temple. It further revealed that it was the place where Goddess Sathi vanished in the altar, renouncing all worldly attachments. The prashnam also concluded that the child should have returned the bowl. As a way of atonement, it was prescribed that the members of the Royal family should refrain from visiting the Kottiyoor temple thereafter. However, the following year, during the Kottiyoor festival, the Raaja forgot this direction and proceeded to the temple with his entourage. On his way, he encountered a serpent blocking his path, and his guard killed it with a sword. But this action led to more serpents appearing one after another, ultimately killing the guard. Suddenly, a many-hooded serpent confronted the Raaja, and in fear, he prostrated on the ground and prayed to the Lord, seeking forgiveness for any misdeeds. In response, he heard a divine voice saying that because he had disobeyed the instructions revealed in the prashnam, he should not visit Kottiyoor. Another prashnam that followed revealed that the Lord was pleased with the Raaja's unwavering faith and decided to make His presence felt at the nearby Sree Mahadeva temple, the ancestral deity of the Raaja's family. The Raaja visited the temple and was astonished to see the Lord's hands atop an arayaal (Baniyan) plant. To commemorate this divine occurrence, the Raaja arranged to pile soil up to the top of the plant where the hands of the Lord were seen, creating a mound known as Thrikkaikunnu. Since then, the temple came to be known by this name. It is believed that the temple properties were originally owned by Nampoothiri families but later came into the possession of the Kottayam Royal family. Presently, the temple is under the ownership of Bhajana Kovilakam (of Kottayam Raajas). The day-to-day administration is overseen by the Secretary with the concurrence of the Raaja on important matters. The Kshethra Samrakshana Samithi, consisting of 15 members elected yearly by devotees, administers the temple with the Raaja's permission.