The current structural temple and the rock-cut sculpture strewn in the vicinity indicate that the temple has been built and renovated many times in the period 8th–9th, 11th–12th, 13th–14th centuries and even later.

Historians have suggested that the Kamakhya temple was likely an ancient sacrificial site for Khasi and Garo peoples and that the name originates in the Khasi goddess, Ka Meikha (literally: old-cousin-mother); and these claims are supported by the folklores of these very peoples.