Daikaku-ji Temple was again completely destroyed by fire during the Onin War but the protection of the Toyotomi clan and Tokugawa clan meant that it was rebuilt and flourished as a monzeki temple until its decline at the end of the Edo period.
応仁の乱では全焼したが、豊臣氏・徳川氏の保護もあり、伽藍を再建し、門跡寺院として繁栄したが、江戸時代末期に衰退した。