Koodalmanikyam Temple history is lost as it was not documented. There is no concrete evidence regarding the origin of Koodalmanikyam temple. Here is a look at some of the important historical aspects of the temple dedicated to Chaturbhuja Vishnu with Conch, Chakra, Gada and Japa Mala. The general belief, however, is that the murti in the temple is Bharatha the brother of Sree Rama.
Thousands of years ago the entire area around Koodalmanikyam temple was a dense forest and a number of Rishis under Kulipini Maharshi were engaged in an incessant Yagna offering severe penance to please Maha Vishnu. Ultimately pleased at the intensity and sincerity of their devotion, Vishnu appeared before them and offered to satisfy their wish. All they wanted was his eternal presence at the place. Bhagavan Vishnu readily agreed. The Rishis now prayed to Goddess Ganga to bless the sacred Yagya Bhoomi with her presence. Answering to the their prayers, springs of River Ganga inundated the area.
The presence of Ganga is believed to continue in the Kulipini Theertham named after the chief of Rishis. This tank on the northern side of the temple is believed to be as sacred as Sreekovil. Water snakes, frogs etc. commonly found in most temple tanks are totally absent here. Only fish grow freely and feeding them is meritorious.
It is believed that the murti gave out unusual brightness from its forehead. A Manikyam or precious stone was the light. But no one was able to identify the stone. Vakaikaimmal the person administering the temple went in search for a similar stone. He found such a similar quartz (Manikyam) in the possession of Raja of Kayamkulam. He got the stone to Koodalmanikyam temple. As he was comparing the brightness of the two, it is said the stone brought from Kayamkulam mysteriously slipped from the hand and merged in the murti. The merging of the two manikyams led to the name 'Koodalmanikyam'. Similar brightness is reported to have appeared on the murti once again 1907.
As per some scholars, Koodalmanikyam is the Malayalam translation of the Sanskrit word Sangameswara.
The earliest historical reference to Koodalmanikyam Temple is found in a stone inscription attributed to the Chera King Sthanu Ravi Varman dated 854 AD, donating vast extents of land for the temple. It is, therefore, reasonable to assume that the Temple must have been in existence for quite some time before this date and that even then Koodalmanikyam was occupying a place of importance among the temples of Kerala.
Another Cheraman Perumal Bhaskara Ravi Varma has donated vast lands at Potta near Chalakudy to the Temple.
The Temple was in the domain of the erstwhile Maharaja of Cochin; but the administration was under a person designated as Thachudaya Kaimal appointed by the Maharaja of Travancore.