In 675 (Tenmu 4), the shrine was relocated from its original site in the Takebe district of Kanzaki County to its present location at Seta. This is considered part of Emperor Tenmu's reorganization of national rites and marked the establishment of Takebe Taisha as the Ichinomiya of Ōmi Province. Seta had been a strategic point on the Tōkaidō and Tōsandō highways since antiquity, lending great significance to the shrine's position as a center of national worship.

In the 8th month of 1180 (Jishō 4), Minamoto no Yoritomo, exiled to Izu, raised arms upon receiving Prince Mochihito's edict. After his defeat at the Battle of Ishibashiyama, he fled to Awa and regrouped. According to tradition, on his march to overthrow the Taira, he visited Takebe Taisha and prayed for the restoration of the Minamoto clan. His prayer to the deity of valor Yamato Takeru was a crucial spiritual rite for the future founder of warrior government, and after the establishment of the Kamakura shogunate, Takebe Taisha continued to receive deep veneration from warrior families.