Once the Muromachi period began, however, Tōdai-ji rapidly lost the vitality of the previous era. Spurring on the decline was the torching of the temple in 1567 by the armies of the Miyoshi and Matsunaga clans. Lost were the Great Buddha Hall, the Ordination Hall, as well as many other structures. The Great Buddha was washed by rains for almost one hundred years.
It was the monk Kōkei who resolved to rebuild the Great Buddha Hall after seeing this miserable sight. Starting in 1686 work to recast the head and eighteen of the petals of the lotus pedestal was begun, and the image was rededicated in 1692. Work on the Great Buddha Hall proceeded simultaneously; the financial conditions of the time, however, did not allow the new structure to match the scale of the Nara and Kamakura period versions. The present hall was rebuilt to a size of about sixty percent of the original in width and was dedicated with great fanfare in 1709.