In 1610, Tokugawa Ieyasu granted temple land in Honjo to Mirokuji as part of his strategic development of the area. Ieyasu carefully planned the placement of temples around Edo Castle, and the Honjo temple district was part of this grand design. Mirokuji is one of the few temples to have received land directly from Ieyasu, demonstrating its strong ties to the shogunate.

Tokugawa Mitsukuni (Mito Komon), the second lord of Mito Domain, donated a Yakushi Nyorai statue to Mirokuji. Mitsukuni, known for his historical compilation project Dai Nihonshi, took deep interest in temples across Edo. The donation of Yakushi Nyorai expressed his prayers for healing and the salvation of all beings.

When Ota Dokan built Edo Castle in 1458, he invited the monk Nichiju to establish this temple at Hirakawaguchi for the castle's spiritual protection and the welfare of the people. After Dokan's death, the temple was renamed Hoonji after his posthumous Buddhist name 'Hoonsai.' The very place name Taihei preserves Dokan's legacy, making this one of the most representative temples connected to the great castle builder.