The earliest historical dynasty of Kamarupa, the Varmans (350-650), as well as Xuanzang, a 7th-century Chinese traveler ignore the Kamakhya; and it is assumed that the worship at least till that period was Kirata-based beyond the brahminical ambit. The later Palas of Kamarupa kings, from Indra Pala to Dharma Pala, were followers of the Tantrik tenet and about that period Kamakhya had become an important seat of Tantrikism.
The Mahant and his successors came to be known as Parbatiya Gosains, as they resided on top of the Nilachal hill.
Many Kamakhya priests and modern Saktas of Assam are either disciples or descendants of the Parbatiya Gosains, or of the Nati and Na Gosains.
Banerji (1925) records that this structure was further built over by the rulers of the Ahom kingdom.
According to historical records and epigraphic evidence, the main temple was rebuilt by Chilarai using the available stone ruins, According to a legend the Koch Bihar royal family was banned by Devi herself from offering puja at the temple.
The ruins of the temple was said to have been discovered by Vishwasingha (1515–1540), the founder of the Koch dynasty, who revived worship at the site; but it was during the reign of his son, Naranarayan (1540–1587), that the temple reconstruction was completed in 1565.