Daikoji Temple, the 67th sacred spot along the Shikoku Henro pilgrimage, was built in 742 (Heian 14) as a sub-temple of Todaiji one kilometer northwest of its current location in an area called Koaza for protection from the Kumano Sansho Gongen (Three Avatars of Kumano). In 792 (Enryaku 11) it was visited by Daishi on a preaching tour, then in 822 (Konin 13) it was restored with an imperial edict by Emperor Saga, then later moved to a small hill surrounded by forest where it currently stands. At the time, there were 24 dwellings of the Shingon Sect and 12 of the Tendai Sect under one roof, and while having such an unusual history of both sects studying within the same precincts, it is currently part of the Shingon Zentsuji Sect. However, the influence of the Tendai Sect was greater, and this temple is arranged like no other, with the main hall sandwiched between the Kobo Daishido Hall dedicated to Kobo Daishi and the Tendai Daishido Hall dedicated to the Chinese Tendai Sect founder Zhiyi. Additionally, Kumano Sansho Gongen was built adjacent to the Daikoji Temple building just south of Kobo Daishido Hall, leaving behind rich traces of Shinto-Buddhist syncretism.

After a fire set by the armies of Chosokabe Morichika, Daikoji Temple once temporarily declined, but it was rebuilt during the Edo Period, with its current main hall originating in 1741 (Kanpo 1). Prefecturally-designated cultural properties stored here include a seated statue of Yakushi Nyorai from the late Heian Period, seated statues of Tendai Daishi, Kobo Daishi, and Nio from the Kamakura Period, and a tablet with the temple name engraving made around the same time. Moreover, the Japanese nutmeg and camphor trees flanking the promenade from the Niomon Gate to the Main Hall are said to have been planted by Daishi himself.