After being destroyed during the Onin War and subsequently rebuilt, the temple enjoyed a brief period of tranquility but was lost to yet another fire in 1815 (Edo period) before being severely damaged during the Hamaguri Rebellion (Conspiracy of Kimmon) of 1864, so that now most of the buildings as we see them today are reconstructions dating from the latter half of the Meiji period.
応仁の乱による焼失・再建後、しばらくは安泰であったが、江戸時代の文化(元号)12年（1815年）にも焼失、さらに幕末の元治元年（1864年）、蛤御門の変（禁門の変）で大打撃を受け、現存伽藍の大部分は明治時代後半以降のものである。