Toyokoto Shrine's principal deity Mori Hidemoto was born to Toda Motokiyo, the fourth son of Mori Motonari — who unified western Japan under the Mori banner. The legacy Motonari built was carried to Nagafu by his grandson Hidemoto, who in 1602 founded Miyazaki Hachimangu (the predecessor of this shrine) upon entering Nagafu castle, enshrining the ancestral Mori tutelary deity in this new domain. Toyokoto Shrine stands as the living testimony of Motonari's bloodline in Nagafu.

Mori Hidemoto was adopted by Mori Terumoto as heir to the Mori clan, but was displaced in 1593 when Terumoto fathered a biological son, Hidenari. In compensation Hidemoto received 60,000 koku in Nagato province and founded the Nagafu domain, establishing Miyazaki Hachimangu — the predecessor of this shrine — in 1602. Toyokoto Shrine thus enshrines the adopted son of Terumoto as its principal deity, marking the genesis of the Nagafu branch of the Mori house. At Sekigahara, Hidemoto is said to have remained on Mt. Nangu with the Western Army but took no decisive action in line with Terumoto's wishes.