It was built in 1344[1][2][3][4] by the Malabari Jews after fleeing from Cranganore, making it the oldest synagogue in India in recorded history.

The compound had at least one intact wall and was colloquially called "Misro Palli" though the entomology of the name is lost to time.

The reason for this migration is unclear with numerous theories and legends ranging from an attack by the Portuguese, a catastrophic flood in 1341, to a quarrel and subsequent murder of his elder brother Aaron Azar.

Another tradition states that the Palayur Jews migrated to Kochangadi and founded the congregation, based on oral songs of Cochini women.

[3] Other traditions state that the nearby Chembittapally, a Muslim mosque, was built with wood donated by the Kochangadi Jews.