From its establishment completion untill the end of Tokugawa Shogunate period, the shrine was a shinto shrine of shinbutsu shugo and was called Iwashimizu Hachimangu Gokokuji Temple, and the shrine is deeply and historically related to many temples such as To-ji (Kyo-o-gokoku-ji), Kiyomizu Temple, Ninna Temple, Rokuon-ji Temple (Shokoku-ji Temple, Kinkaku-ji Temple, Ginkakuji-Temple).
創建以来、幕末までは神仏習合の宮寺で石清水八幡宮護国寺と称し、東寺（教王護国寺）や清水寺、比叡山延暦寺、仁和寺、鹿苑寺（相国寺・金閣寺・銀閣寺）など、多くの寺院との歴史的関連が深い。