In 857, by opportunity of a visit to the temple by the monk Ennin (793 or 794–864), Nihon-ji was transferred to the Tendai school of Buddhism.

Nihon-ji was burned during a local conflict 1331 and many of the temple structures, including the dōu hall, were destroyed.

Takauji built the dōu (堂宇) eaved main hall in 1345, but during the Sengoku period the temple again fell into decline.

In the Tenshō era (1573–1592) of the Momoyama period, Nihon-ji came under the protection of the powerful Satomi clan of Awa Province.

The chief dōu hall, statues, and treasured Buddhist articles were lost in a fire that occurred due to the earthquake.

In 1989, the government of India presented Nihon-ji with a sapling from the Bodhi tree as a gesture of world peace.

[citation needed] In 2007, another round of reconstruction efforts targeting the temple's structures was completed, rebuilding the Bhaisajyaguru Hall and several other buildings.