The temple's origins are ancient, rooted in the indigenous Khasi belief in sacred natural formations. The cave and its stalagmite were revered by the local Khasi people long before the arrival of Hinduism in the region. The Sanskritization of the site — where the natural stalagmite came to be worshipped as a Shiva Lingam — occurred gradually over the past few centuries as Hindu influence spread through the northeastern region.
The current temple management was formalized in the 20th century by local Hindu communities with support from the Meghalaya state government. The cave has been a protected site under the Meghalaya tourism department and has gained international recognition as a unique natural-spiritual destination. The temple is maintained by the Mawjymbuin Temple Trust, which oversees both the cave's preservation and its religious functions.
