[3] During the Muromachi period, the temple was devastated by the Ōnin War, leaving only the five-storied pagoda as the sole surviving structure.

In 1939, a forest fire struck the Kami-Daigo portion of the temple, burning down the Buddhist Texts Library and the Juntei-dō, which was only rebuilt in 1968.

Wall paintings at the temple were the subject of academic research which earned the Imperial Prize of the Japan Academy in 1960.

More than seven centuries after its founding, Toyotomi Hideyoshi held a famous cherry blossom viewing party called Daigo no hanami[5] in 1598 at the Sambō-in sub-temple.

It contains the temple proper (including a noted tea garden), a museum, and other complexes, and is very lively during cherry blossom season.

Shimo-Daigo is one large enclosure, containing detached halls, including the oldest surviving building in Kyoto, together with open spaces.

There is a path with stairs up to the top, which takes about one hour to reach the main complex; halfway up there is a resting point and small shrine.

[9] This resulted in the temporary closure of the upper area (Kami Daigo-ji) for disaster restoration construction, which reopened on July 1, 2009.